Compare the DEGs obtained across time points and produce related visualizations.
Approaches
Basic DEA vs DMSO
Basic DEA Agonist vs Inhibitor
Analyses are performed for all pathways or a selected subset (estrogen, retionic, thyroid, liverX).
::opts_chunk$set(echo = TRUE, warning=FALSE, collapse = TRUE) knitr
library(tidyr)
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(ggplot2)
library(GeneOverlap)
<- params$OutputFolder OutputFolder
<- readRDS(paste0(params$InputFolder, 'DEARes.rds')) DEA
<- list(
DEGs_Agonist
Thyr_Ag_Up= row.names(DEA$Thyr$Agonist$DEGs[DEA$Thyr$Agonist$DEGs$log2FoldChange > 0, ]),
Thyr_Ag_Down= row.names(DEA$Thyr$Agonist$DEGs[DEA$Thyr$Agonist$DEGs$log2FoldChange < 0, ]),
Ret_Ag_Up= row.names(DEA$Ret$Agonist$DEGs[DEA$Ret$Agonist$DEGs$log2FoldChange > 0, ]),
Ret_Ag_Down= row.names(DEA$Ret$Agonist$DEGs[DEA$Ret$Agonist$DEGs$log2FoldChange < 0, ]),
Estr_Ag_Up= row.names(DEA$Estr$Agonist$DEGs[DEA$Estr$Agonist$DEGs$log2FoldChange > 0, ]),
Estr_Ag_Down= row.names(DEA$Estr$Agonist$DEGs[DEA$Estr$Agonist$DEGs$log2FoldChange < 0, ]),
Andr_Ag_Up= row.names(DEA$Andr$Agonist$DEGs[DEA$Andr$Agonist$DEGs$log2FoldChange > 0, ]),
Andr_Ag_Down= row.names(DEA$Andr$Agonist$DEGs[DEA$Andr$Agonist$DEGs$log2FoldChange < 0, ]),
GC_Ag_Up= row.names(DEA$GC$Agonist$DEGs[DEA$GC$Agonist$DEGs$log2FoldChange > 0, ]),
GC_Ag_Down= row.names(DEA$GC$Agonist$DEGs[DEA$GC$Agonist$DEGs$log2FoldChange < 0, ]),
LivX_Ag_Up= row.names(DEA$LivX$Agonist$DEGs[DEA$LivX$Agonist$DEGs$log2FoldChange > 0, ]),
LivX_Ag_Down= row.names(DEA$LivX$Agonist$DEGs[DEA$LivX$Agonist$DEGs$log2FoldChange < 0, ]),
AhHyd_Ag_Up= row.names(DEA$AhHyd$Agonist$DEGs[DEA$AhHyd$Agonist$DEGs$log2FoldChange > 0, ]),
AhHyd_Ag_Down= row.names(DEA$AhHyd$Agonist$DEGs[DEA$AhHyd$Agonist$DEGs$log2FoldChange < 0, ])
)
<- row.names(DEA$Ret$Agonist$Res) %>% unique()
Universe ## Loading required package: DESeq2
## Loading required package: S4Vectors
## Loading required package: stats4
## Loading required package: BiocGenerics
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## Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
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## Loading required package: GenomicRanges
## Loading required package: GenomeInfoDb
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## Loading required package: matrixStats
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## Loading required package: Biobase
## Welcome to Bioconductor
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## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.
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length(Universe)
## [1] 14305
<- newGOM(DEGs_Agonist, DEGs_Agonist, genome.size=length(Universe))
OvObj print(OvObj)
## A GeneOverlapMatrix object:
## ###### Intersection ######
## Thyr_Ag_Up Thyr_Ag_Down Ret_Ag_Up Ret_Ag_Down Estr_Ag_Up
## Thyr_Ag_Up 78 0 48 17 1
## Thyr_Ag_Down 0 69 11 36 0
## Ret_Ag_Up 48 11 1861 0 1
## Ret_Ag_Down 17 36 0 1108 0
## Estr_Ag_Up 1 0 1 0 1
## Estr_Ag_Down 0 2 1 0 0
## Andr_Ag_Up 3 3 58 7 1
## Andr_Ag_Down 0 2 16 5 0
## GC_Ag_Up 1 0 4 0 1
## GC_Ag_Down 0 2 4 1 0
## LivX_Ag_Up 1 0 2 0 1
## LivX_Ag_Down 1 1 4 0 0
## AhHyd_Ag_Up 2 1 2 9 1
## AhHyd_Ag_Down 2 5 30 12 0
## Estr_Ag_Down Andr_Ag_Up Andr_Ag_Down GC_Ag_Up GC_Ag_Down
## Thyr_Ag_Up 0 3 0 1 0
## Thyr_Ag_Down 2 3 2 0 2
## Ret_Ag_Up 1 58 16 4 4
## Ret_Ag_Down 0 7 5 0 1
## Estr_Ag_Up 0 1 0 1 0
## Estr_Ag_Down 3 2 0 0 1
## Andr_Ag_Up 2 197 0 3 5
## Andr_Ag_Down 0 0 45 0 1
## GC_Ag_Up 0 3 0 6 0
## GC_Ag_Down 1 5 1 0 13
## LivX_Ag_Up 0 1 0 1 0
## LivX_Ag_Down 1 2 0 0 3
## AhHyd_Ag_Up 0 3 0 1 0
## AhHyd_Ag_Down 0 0 2 0 0
## LivX_Ag_Up LivX_Ag_Down AhHyd_Ag_Up AhHyd_Ag_Down
## Thyr_Ag_Up 1 1 2 2
## Thyr_Ag_Down 0 1 1 5
## Ret_Ag_Up 2 4 2 30
## Ret_Ag_Down 0 0 9 12
## Estr_Ag_Up 1 0 1 0
## Estr_Ag_Down 0 1 0 0
## Andr_Ag_Up 1 2 3 0
## Andr_Ag_Down 0 0 0 2
## GC_Ag_Up 1 0 1 0
## GC_Ag_Down 0 3 0 0
## LivX_Ag_Up 10 0 1 0
## LivX_Ag_Down 0 6 0 0
## AhHyd_Ag_Up 1 0 20 0
## AhHyd_Ag_Down 0 0 0 56
## ###### P-value ######
## Thyr_Ag_Up Thyr_Ag_Down Ret_Ag_Up Ret_Ag_Down
## Thyr_Ag_Up 1.040621e-209 1.000000e+00 1.137907e-23 7.805123e-05
## Thyr_Ag_Down 1.000000e+00 3.766883e-189 2.819577e-01 2.579072e-22
## Ret_Ag_Up 1.137907e-23 2.819577e-01 0.000000e+00 1.000000e+00
## Ret_Ag_Down 7.805123e-05 2.579072e-22 1.000000e+00 0.000000e+00
## Estr_Ag_Up 5.452639e-03 1.000000e+00 1.300944e-01 1.000000e+00
## Estr_Ag_Down 1.000000e+00 6.857653e-05 3.417319e-01 1.000000e+00
## Andr_Ag_Up 9.265938e-02 6.965485e-02 8.016126e-10 9.951476e-01
## Andr_Ag_Down 1.000000e+00 1.986370e-02 9.868927e-05 2.675348e-01
## GC_Ag_Up 3.227866e-02 1.000000e+00 3.442533e-03 1.000000e+00
## GC_Ag_Down 1.000000e+00 1.728186e-03 7.772264e-02 6.495414e-01
## LivX_Ag_Up 5.322409e-02 1.000000e+00 3.807545e-01 1.000000e+00
## LivX_Ag_Down 3.227866e-02 2.859911e-02 3.442533e-03 1.000000e+00
## AhHyd_Ag_Up 5.232939e-03 9.223306e-02 7.544395e-01 7.453704e-06
## AhHyd_Ag_Down 3.739553e-02 7.114372e-06 4.642748e-13 1.007141e-03
## Estr_Ag_Up Estr_Ag_Down Andr_Ag_Up Andr_Ag_Down GC_Ag_Up
## Thyr_Ag_Up 5.452639e-03 1.000000e+00 9.265938e-02 1.000000e+00 3.227866e-02
## Thyr_Ag_Down 1.000000e+00 6.857653e-05 6.965485e-02 1.986370e-02 1.000000e+00
## Ret_Ag_Up 1.300944e-01 3.417319e-01 8.016126e-10 9.868927e-05 3.442533e-03
## Ret_Ag_Down 1.000000e+00 1.000000e+00 9.951476e-01 2.675348e-01 1.000000e+00
## Estr_Ag_Up 6.990563e-05 1.000000e+00 1.377141e-02 1.000000e+00 4.194338e-04
## Estr_Ag_Down 1.000000e+00 2.050117e-12 5.609612e-04 1.000000e+00 1.000000e+00
## Andr_Ag_Up 1.377141e-02 5.609612e-04 0.000000e+00 1.000000e+00 4.989996e-05
## Andr_Ag_Down 1.000000e+00 1.000000e+00 1.000000e+00 1.291057e-131 1.000000e+00
## GC_Ag_Up 4.194338e-04 1.000000e+00 4.989996e-05 1.000000e+00 8.411255e-23
## GC_Ag_Down 1.000000e+00 2.724033e-03 5.539904e-07 4.014828e-02 1.000000e+00
## LivX_Ag_Up 6.990563e-04 1.000000e+00 1.295240e-01 1.000000e+00 4.187745e-03
## LivX_Ag_Down 1.000000e+00 1.257861e-03 2.729185e-03 1.000000e+00 1.000000e+00
## AhHyd_Ag_Up 1.398113e-03 1.000000e+00 2.467071e-03 1.000000e+00 8.360865e-03
## AhHyd_Ag_Down 1.000000e+00 1.000000e+00 1.000000e+00 1.337955e-02 1.000000e+00
## GC_Ag_Down LivX_Ag_Up LivX_Ag_Down AhHyd_Ag_Up AhHyd_Ag_Down
## Thyr_Ag_Up 1.000000e+00 5.322409e-02 3.227866e-02 5.232939e-03 3.739553e-02
## Thyr_Ag_Down 1.728186e-03 1.000000e+00 2.859911e-02 9.223306e-02 7.114372e-06
## Ret_Ag_Up 7.772264e-02 3.807545e-01 3.442533e-03 7.544395e-01 4.642748e-13
## Ret_Ag_Down 6.495414e-01 1.000000e+00 1.000000e+00 7.453704e-06 1.007141e-03
## Estr_Ag_Up 1.000000e+00 6.990563e-04 1.000000e+00 1.398113e-03 1.000000e+00
## Estr_Ag_Down 2.724033e-03 1.000000e+00 1.257861e-03 1.000000e+00 1.000000e+00
## Andr_Ag_Up 5.539904e-07 1.295240e-01 2.729185e-03 2.467071e-03 1.000000e+00
## Andr_Ag_Down 4.014828e-02 1.000000e+00 1.000000e+00 1.000000e+00 1.337955e-02
## GC_Ag_Up 1.000000e+00 4.187745e-03 1.000000e+00 8.360865e-03 1.000000e+00
## GC_Ag_Down 5.960832e-45 1.000000e+00 1.170823e-08 1.000000e+00 1.000000e+00
## LivX_Ag_Up 1.000000e+00 1.014497e-35 1.000000e+00 1.389784e-02 1.000000e+00
## LivX_Ag_Down 1.170823e-08 1.000000e+00 8.411255e-23 1.000000e+00 1.000000e+00
## AhHyd_Ag_Up 1.000000e+00 1.389784e-02 1.000000e+00 1.914866e-65 1.000000e+00
## AhHyd_Ag_Down 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.553685e-158
## ###### Odds Ratio ######
## Thyr_Ag_Up Thyr_Ag_Down Ret_Ag_Up Ret_Ag_Down Estr_Ag_Up
## Thyr_Ag_Up Inf 0.000000 10.9510459 3.3550283 Inf
## Thyr_Ag_Down 0.000000 Inf 1.2697431 13.3903265 0
## Ret_Ag_Up 10.951046 1.269743 Inf 0.0000000 Inf
## Ret_Ag_Down 3.355028 13.390327 0.0000000 Inf 0
## Estr_Ag_Up Inf 0.000000 Inf 0.0000000 Inf
## Estr_Ag_Down 0.000000 419.587900 3.3442545 0.0000000 0
## Andr_Ag_Up 2.892986 3.289530 2.8474388 0.4352635 Inf
## Andr_Ag_Down 0.000000 9.846678 3.7124461 1.4909839 0
## GC_Ag_Up 36.835016 0.000000 13.3957228 0.0000000 Inf
## GC_Ag_Down 0.000000 38.505367 2.9758029 0.9925479 0
## LivX_Ag_Up 20.501898 0.000000 1.6723256 0.0000000 Inf
## LivX_Ag_Down 36.835016 41.741898 13.3957228 0.0000000 0
## AhHyd_Ag_Up 20.736391 10.997978 0.7427073 9.8136457 Inf
## AhHyd_Ag_Down 6.902948 21.699494 7.8218662 3.2725273 0
## Estr_Ag_Down Andr_Ag_Up Andr_Ag_Down GC_Ag_Up GC_Ag_Down
## Thyr_Ag_Up 0.000000 2.8929860 0.000000 36.83502 0.0000000
## Thyr_Ag_Down 419.587900 3.2895301 9.846678 0.00000 38.5053671
## Ret_Ag_Up 3.344255 2.8474388 3.712446 13.39572 2.9758029
## Ret_Ag_Down 0.000000 0.4352635 1.490984 0.00000 0.9925479
## Estr_Ag_Up 0.000000 Inf 0.000000 Inf 0.0000000
## Estr_Ag_Down Inf 143.8041372 0.000000 0.00000 572.4231226
## Andr_Ag_Up 143.804137 Inf 0.000000 72.58376 45.8103110
## Andr_Ag_Down 0.000000 0.0000000 Inf 0.00000 26.9525489
## GC_Ag_Up 0.000000 72.5837635 0.000000 Inf 0.0000000
## GC_Ag_Down 572.423123 45.8103110 26.952549 0.00000 Inf
## LivX_Ag_Up 0.000000 7.9892731 0.000000 315.81514 0.0000000
## LivX_Ag_Down 1380.290241 36.1085325 0.000000 0.00000 1338.8541918
## AhHyd_Ag_Up 0.000000 12.8099630 0.000000 148.99012 0.0000000
## AhHyd_Ag_Down 0.000000 0.0000000 12.226893 0.00000 0.0000000
## LivX_Ag_Up LivX_Ag_Down AhHyd_Ag_Up AhHyd_Ag_Down
## Thyr_Ag_Up 20.501898 36.83502 20.7363905 6.902948
## Thyr_Ag_Down 0.000000 41.74190 10.9979777 21.699494
## Ret_Ag_Up 1.672326 13.39572 0.7427073 7.821866
## Ret_Ag_Down 0.000000 0.00000 9.8136457 3.272527
## Estr_Ag_Up Inf 0.00000 Inf 0.000000
## Estr_Ag_Down 0.000000 1380.29024 0.0000000 0.000000
## Andr_Ag_Up 7.989273 36.10853 12.8099630 0.000000
## Andr_Ag_Down 0.000000 0.00000 0.0000000 12.226893
## GC_Ag_Up 315.815143 0.00000 148.9901154 0.000000
## GC_Ag_Down 0.000000 1338.85419 0.0000000 0.000000
## LivX_Ag_Up Inf 0.00000 83.1198722 0.000000
## LivX_Ag_Down 0.000000 Inf 0.0000000 0.000000
## AhHyd_Ag_Up 83.119872 0.00000 Inf 0.000000
## AhHyd_Ag_Down 0.000000 0.00000 0.0000000 Inf
## ###### Jaccard Index ######
## Thyr_Ag_Up Thyr_Ag_Down Ret_Ag_Up Ret_Ag_Down Estr_Ag_Up
## Thyr_Ag_Up 1.00000000 0.000000000 0.0253833950 0.0145423439 0.0128205128
## Thyr_Ag_Down 0.00000000 1.000000000 0.0057321522 0.0315512708 0.0000000000
## Ret_Ag_Up 0.02538340 0.005732152 1.0000000000 0.0000000000 0.0005373455
## Ret_Ag_Down 0.01454234 0.031551271 0.0000000000 1.0000000000 0.0000000000
## Estr_Ag_Up 0.01282051 0.000000000 0.0005373455 0.0000000000 1.0000000000
## Estr_Ag_Down 0.00000000 0.028571429 0.0005367687 0.0000000000 0.0000000000
## Andr_Ag_Up 0.01102941 0.011406844 0.0290000000 0.0053929122 0.0050761421
## Andr_Ag_Down 0.00000000 0.017857143 0.0084656085 0.0043554007 0.0000000000
## GC_Ag_Up 0.01204819 0.000000000 0.0021470746 0.0000000000 0.1666666667
## GC_Ag_Down 0.00000000 0.025000000 0.0021390374 0.0008928571 0.0000000000
## LivX_Ag_Up 0.01149425 0.000000000 0.0010700910 0.0000000000 0.1000000000
## LivX_Ag_Down 0.01204819 0.013513514 0.0021470746 0.0000000000 0.0000000000
## AhHyd_Ag_Up 0.02083333 0.011363636 0.0010643960 0.0080428954 0.0500000000
## AhHyd_Ag_Down 0.01515152 0.041666667 0.0158982512 0.0104166667 0.0000000000
## Estr_Ag_Down Andr_Ag_Up Andr_Ag_Down GC_Ag_Up GC_Ag_Down
## Thyr_Ag_Up 0.0000000000 0.011029412 0.000000000 0.012048193 0.0000000000
## Thyr_Ag_Down 0.0285714286 0.011406844 0.017857143 0.000000000 0.0250000000
## Ret_Ag_Up 0.0005367687 0.029000000 0.008465608 0.002147075 0.0021390374
## Ret_Ag_Down 0.0000000000 0.005392912 0.004355401 0.000000000 0.0008928571
## Estr_Ag_Up 0.0000000000 0.005076142 0.000000000 0.166666667 0.0000000000
## Estr_Ag_Down 1.0000000000 0.010101010 0.000000000 0.000000000 0.0666666667
## Andr_Ag_Up 0.0101010101 1.000000000 0.000000000 0.015000000 0.0243902439
## Andr_Ag_Down 0.0000000000 0.000000000 1.000000000 0.000000000 0.0175438596
## GC_Ag_Up 0.0000000000 0.015000000 0.000000000 1.000000000 0.0000000000
## GC_Ag_Down 0.0666666667 0.024390244 0.017543860 0.000000000 1.0000000000
## LivX_Ag_Up 0.0000000000 0.004854369 0.000000000 0.066666667 0.0000000000
## LivX_Ag_Down 0.1250000000 0.009950249 0.000000000 0.000000000 0.1875000000
## AhHyd_Ag_Up 0.0000000000 0.014018692 0.000000000 0.040000000 0.0000000000
## AhHyd_Ag_Down 0.0000000000 0.000000000 0.020202020 0.000000000 0.0000000000
## LivX_Ag_Up LivX_Ag_Down AhHyd_Ag_Up AhHyd_Ag_Down
## Thyr_Ag_Up 0.011494253 0.012048193 0.020833333 0.01515152
## Thyr_Ag_Down 0.000000000 0.013513514 0.011363636 0.04166667
## Ret_Ag_Up 0.001070091 0.002147075 0.001064396 0.01589825
## Ret_Ag_Down 0.000000000 0.000000000 0.008042895 0.01041667
## Estr_Ag_Up 0.100000000 0.000000000 0.050000000 0.00000000
## Estr_Ag_Down 0.000000000 0.125000000 0.000000000 0.00000000
## Andr_Ag_Up 0.004854369 0.009950249 0.014018692 0.00000000
## Andr_Ag_Down 0.000000000 0.000000000 0.000000000 0.02020202
## GC_Ag_Up 0.066666667 0.000000000 0.040000000 0.00000000
## GC_Ag_Down 0.000000000 0.187500000 0.000000000 0.00000000
## LivX_Ag_Up 1.000000000 0.000000000 0.034482759 0.00000000
## LivX_Ag_Down 0.000000000 1.000000000 0.000000000 0.00000000
## AhHyd_Ag_Up 0.034482759 0.000000000 1.000000000 0.00000000
## AhHyd_Ag_Down 0.000000000 0.000000000 0.000000000 1.00000000
getMatrix(OvObj, name='intersection')
## Thyr_Ag_Up Thyr_Ag_Down Ret_Ag_Up Ret_Ag_Down Estr_Ag_Up
## Thyr_Ag_Up 78 0 48 17 1
## Thyr_Ag_Down 0 69 11 36 0
## Ret_Ag_Up 48 11 1861 0 1
## Ret_Ag_Down 17 36 0 1108 0
## Estr_Ag_Up 1 0 1 0 1
## Estr_Ag_Down 0 2 1 0 0
## Andr_Ag_Up 3 3 58 7 1
## Andr_Ag_Down 0 2 16 5 0
## GC_Ag_Up 1 0 4 0 1
## GC_Ag_Down 0 2 4 1 0
## LivX_Ag_Up 1 0 2 0 1
## LivX_Ag_Down 1 1 4 0 0
## AhHyd_Ag_Up 2 1 2 9 1
## AhHyd_Ag_Down 2 5 30 12 0
## Estr_Ag_Down Andr_Ag_Up Andr_Ag_Down GC_Ag_Up GC_Ag_Down
## Thyr_Ag_Up 0 3 0 1 0
## Thyr_Ag_Down 2 3 2 0 2
## Ret_Ag_Up 1 58 16 4 4
## Ret_Ag_Down 0 7 5 0 1
## Estr_Ag_Up 0 1 0 1 0
## Estr_Ag_Down 3 2 0 0 1
## Andr_Ag_Up 2 197 0 3 5
## Andr_Ag_Down 0 0 45 0 1
## GC_Ag_Up 0 3 0 6 0
## GC_Ag_Down 1 5 1 0 13
## LivX_Ag_Up 0 1 0 1 0
## LivX_Ag_Down 1 2 0 0 3
## AhHyd_Ag_Up 0 3 0 1 0
## AhHyd_Ag_Down 0 0 2 0 0
## LivX_Ag_Up LivX_Ag_Down AhHyd_Ag_Up AhHyd_Ag_Down
## Thyr_Ag_Up 1 1 2 2
## Thyr_Ag_Down 0 1 1 5
## Ret_Ag_Up 2 4 2 30
## Ret_Ag_Down 0 0 9 12
## Estr_Ag_Up 1 0 1 0
## Estr_Ag_Down 0 1 0 0
## Andr_Ag_Up 1 2 3 0
## Andr_Ag_Down 0 0 0 2
## GC_Ag_Up 1 0 1 0
## GC_Ag_Down 0 3 0 0
## LivX_Ag_Up 10 0 1 0
## LivX_Ag_Down 0 6 0 0
## AhHyd_Ag_Up 1 0 20 0
## AhHyd_Ag_Down 0 0 0 56
getMatrix(OvObj, name='pval')
## Thyr_Ag_Up Thyr_Ag_Down Ret_Ag_Up Ret_Ag_Down
## Thyr_Ag_Up 1.040621e-209 1.000000e+00 1.137907e-23 7.805123e-05
## Thyr_Ag_Down 1.000000e+00 3.766883e-189 2.819577e-01 2.579072e-22
## Ret_Ag_Up 1.137907e-23 2.819577e-01 0.000000e+00 1.000000e+00
## Ret_Ag_Down 7.805123e-05 2.579072e-22 1.000000e+00 0.000000e+00
## Estr_Ag_Up 5.452639e-03 1.000000e+00 1.300944e-01 1.000000e+00
## Estr_Ag_Down 1.000000e+00 6.857653e-05 3.417319e-01 1.000000e+00
## Andr_Ag_Up 9.265938e-02 6.965485e-02 8.016126e-10 9.951476e-01
## Andr_Ag_Down 1.000000e+00 1.986370e-02 9.868927e-05 2.675348e-01
## GC_Ag_Up 3.227866e-02 1.000000e+00 3.442533e-03 1.000000e+00
## GC_Ag_Down 1.000000e+00 1.728186e-03 7.772264e-02 6.495414e-01
## LivX_Ag_Up 5.322409e-02 1.000000e+00 3.807545e-01 1.000000e+00
## LivX_Ag_Down 3.227866e-02 2.859911e-02 3.442533e-03 1.000000e+00
## AhHyd_Ag_Up 5.232939e-03 9.223306e-02 7.544395e-01 7.453704e-06
## AhHyd_Ag_Down 3.739553e-02 7.114372e-06 4.642748e-13 1.007141e-03
## Estr_Ag_Up Estr_Ag_Down Andr_Ag_Up Andr_Ag_Down GC_Ag_Up
## Thyr_Ag_Up 5.452639e-03 1.000000e+00 9.265938e-02 1.000000e+00 3.227866e-02
## Thyr_Ag_Down 1.000000e+00 6.857653e-05 6.965485e-02 1.986370e-02 1.000000e+00
## Ret_Ag_Up 1.300944e-01 3.417319e-01 8.016126e-10 9.868927e-05 3.442533e-03
## Ret_Ag_Down 1.000000e+00 1.000000e+00 9.951476e-01 2.675348e-01 1.000000e+00
## Estr_Ag_Up 6.990563e-05 1.000000e+00 1.377141e-02 1.000000e+00 4.194338e-04
## Estr_Ag_Down 1.000000e+00 2.050117e-12 5.609612e-04 1.000000e+00 1.000000e+00
## Andr_Ag_Up 1.377141e-02 5.609612e-04 0.000000e+00 1.000000e+00 4.989996e-05
## Andr_Ag_Down 1.000000e+00 1.000000e+00 1.000000e+00 1.291057e-131 1.000000e+00
## GC_Ag_Up 4.194338e-04 1.000000e+00 4.989996e-05 1.000000e+00 8.411255e-23
## GC_Ag_Down 1.000000e+00 2.724033e-03 5.539904e-07 4.014828e-02 1.000000e+00
## LivX_Ag_Up 6.990563e-04 1.000000e+00 1.295240e-01 1.000000e+00 4.187745e-03
## LivX_Ag_Down 1.000000e+00 1.257861e-03 2.729185e-03 1.000000e+00 1.000000e+00
## AhHyd_Ag_Up 1.398113e-03 1.000000e+00 2.467071e-03 1.000000e+00 8.360865e-03
## AhHyd_Ag_Down 1.000000e+00 1.000000e+00 1.000000e+00 1.337955e-02 1.000000e+00
## GC_Ag_Down LivX_Ag_Up LivX_Ag_Down AhHyd_Ag_Up AhHyd_Ag_Down
## Thyr_Ag_Up 1.000000e+00 5.322409e-02 3.227866e-02 5.232939e-03 3.739553e-02
## Thyr_Ag_Down 1.728186e-03 1.000000e+00 2.859911e-02 9.223306e-02 7.114372e-06
## Ret_Ag_Up 7.772264e-02 3.807545e-01 3.442533e-03 7.544395e-01 4.642748e-13
## Ret_Ag_Down 6.495414e-01 1.000000e+00 1.000000e+00 7.453704e-06 1.007141e-03
## Estr_Ag_Up 1.000000e+00 6.990563e-04 1.000000e+00 1.398113e-03 1.000000e+00
## Estr_Ag_Down 2.724033e-03 1.000000e+00 1.257861e-03 1.000000e+00 1.000000e+00
## Andr_Ag_Up 5.539904e-07 1.295240e-01 2.729185e-03 2.467071e-03 1.000000e+00
## Andr_Ag_Down 4.014828e-02 1.000000e+00 1.000000e+00 1.000000e+00 1.337955e-02
## GC_Ag_Up 1.000000e+00 4.187745e-03 1.000000e+00 8.360865e-03 1.000000e+00
## GC_Ag_Down 5.960832e-45 1.000000e+00 1.170823e-08 1.000000e+00 1.000000e+00
## LivX_Ag_Up 1.000000e+00 1.014497e-35 1.000000e+00 1.389784e-02 1.000000e+00
## LivX_Ag_Down 1.170823e-08 1.000000e+00 8.411255e-23 1.000000e+00 1.000000e+00
## AhHyd_Ag_Up 1.000000e+00 1.389784e-02 1.000000e+00 1.914866e-65 1.000000e+00
## AhHyd_Ag_Down 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.553685e-158
getMatrix(OvObj, name='odds.ratio')
## Thyr_Ag_Up Thyr_Ag_Down Ret_Ag_Up Ret_Ag_Down Estr_Ag_Up
## Thyr_Ag_Up Inf 0.000000 10.9510459 3.3550283 Inf
## Thyr_Ag_Down 0.000000 Inf 1.2697431 13.3903265 0
## Ret_Ag_Up 10.951046 1.269743 Inf 0.0000000 Inf
## Ret_Ag_Down 3.355028 13.390327 0.0000000 Inf 0
## Estr_Ag_Up Inf 0.000000 Inf 0.0000000 Inf
## Estr_Ag_Down 0.000000 419.587900 3.3442545 0.0000000 0
## Andr_Ag_Up 2.892986 3.289530 2.8474388 0.4352635 Inf
## Andr_Ag_Down 0.000000 9.846678 3.7124461 1.4909839 0
## GC_Ag_Up 36.835016 0.000000 13.3957228 0.0000000 Inf
## GC_Ag_Down 0.000000 38.505367 2.9758029 0.9925479 0
## LivX_Ag_Up 20.501898 0.000000 1.6723256 0.0000000 Inf
## LivX_Ag_Down 36.835016 41.741898 13.3957228 0.0000000 0
## AhHyd_Ag_Up 20.736391 10.997978 0.7427073 9.8136457 Inf
## AhHyd_Ag_Down 6.902948 21.699494 7.8218662 3.2725273 0
## Estr_Ag_Down Andr_Ag_Up Andr_Ag_Down GC_Ag_Up GC_Ag_Down
## Thyr_Ag_Up 0.000000 2.8929860 0.000000 36.83502 0.0000000
## Thyr_Ag_Down 419.587900 3.2895301 9.846678 0.00000 38.5053671
## Ret_Ag_Up 3.344255 2.8474388 3.712446 13.39572 2.9758029
## Ret_Ag_Down 0.000000 0.4352635 1.490984 0.00000 0.9925479
## Estr_Ag_Up 0.000000 Inf 0.000000 Inf 0.0000000
## Estr_Ag_Down Inf 143.8041372 0.000000 0.00000 572.4231226
## Andr_Ag_Up 143.804137 Inf 0.000000 72.58376 45.8103110
## Andr_Ag_Down 0.000000 0.0000000 Inf 0.00000 26.9525489
## GC_Ag_Up 0.000000 72.5837635 0.000000 Inf 0.0000000
## GC_Ag_Down 572.423123 45.8103110 26.952549 0.00000 Inf
## LivX_Ag_Up 0.000000 7.9892731 0.000000 315.81514 0.0000000
## LivX_Ag_Down 1380.290241 36.1085325 0.000000 0.00000 1338.8541918
## AhHyd_Ag_Up 0.000000 12.8099630 0.000000 148.99012 0.0000000
## AhHyd_Ag_Down 0.000000 0.0000000 12.226893 0.00000 0.0000000
## LivX_Ag_Up LivX_Ag_Down AhHyd_Ag_Up AhHyd_Ag_Down
## Thyr_Ag_Up 20.501898 36.83502 20.7363905 6.902948
## Thyr_Ag_Down 0.000000 41.74190 10.9979777 21.699494
## Ret_Ag_Up 1.672326 13.39572 0.7427073 7.821866
## Ret_Ag_Down 0.000000 0.00000 9.8136457 3.272527
## Estr_Ag_Up Inf 0.00000 Inf 0.000000
## Estr_Ag_Down 0.000000 1380.29024 0.0000000 0.000000
## Andr_Ag_Up 7.989273 36.10853 12.8099630 0.000000
## Andr_Ag_Down 0.000000 0.00000 0.0000000 12.226893
## GC_Ag_Up 315.815143 0.00000 148.9901154 0.000000
## GC_Ag_Down 0.000000 1338.85419 0.0000000 0.000000
## LivX_Ag_Up Inf 0.00000 83.1198722 0.000000
## LivX_Ag_Down 0.000000 Inf 0.0000000 0.000000
## AhHyd_Ag_Up 83.119872 0.00000 Inf 0.000000
## AhHyd_Ag_Down 0.000000 0.00000 0.0000000 Inf
<- data.frame(getMatrix(OvObj, name='odds.ratio'))
OR $DEGs <- row.names(OR)
OR<- gather(OR, 'KBase', 'OR', -DEGs)
OR <- data.frame(getMatrix(OvObj, name='pval'))
PVAL $DEGs <- row.names(PVAL)
PVAL<- gather(PVAL, 'KBase', 'PVal', -DEGs)
PVAL <- data.frame(getMatrix(OvObj, name='intersection'))
NUM $DEGs <- row.names(NUM)
NUM<- gather(NUM, 'KBase', 'Numbers', -DEGs)
NUM if(! identical(OR$DEGs, PVAL$DEGs)){
stop('Inconsistecy')
}if(! identical(OR$DEGs, NUM$DEGs)){
stop('Inconsistecy')
}if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}<- mutate(OR, Pval=PVAL$PVal) %>% mutate(Numbers=NUM$Numbers)
Res
Res## DEGs KBase OR Pval Numbers
## 1 Thyr_Ag_Up Thyr_Ag_Up Inf 1.040621e-209 78
## 2 Thyr_Ag_Down Thyr_Ag_Up 0.0000000 1.000000e+00 0
## 3 Ret_Ag_Up Thyr_Ag_Up 10.9510459 1.137907e-23 48
## 4 Ret_Ag_Down Thyr_Ag_Up 3.3550283 7.805123e-05 17
## 5 Estr_Ag_Up Thyr_Ag_Up Inf 5.452639e-03 1
## 6 Estr_Ag_Down Thyr_Ag_Up 0.0000000 1.000000e+00 0
## 7 Andr_Ag_Up Thyr_Ag_Up 2.8929860 9.265938e-02 3
## 8 Andr_Ag_Down Thyr_Ag_Up 0.0000000 1.000000e+00 0
## 9 GC_Ag_Up Thyr_Ag_Up 36.8350164 3.227866e-02 1
## 10 GC_Ag_Down Thyr_Ag_Up 0.0000000 1.000000e+00 0
## 11 LivX_Ag_Up Thyr_Ag_Up 20.5018984 5.322409e-02 1
## 12 LivX_Ag_Down Thyr_Ag_Up 36.8350164 3.227866e-02 1
## 13 AhHyd_Ag_Up Thyr_Ag_Up 20.7363905 5.232939e-03 2
## 14 AhHyd_Ag_Down Thyr_Ag_Up 6.9029478 3.739553e-02 2
## 15 Thyr_Ag_Up Thyr_Ag_Down 0.0000000 1.000000e+00 0
## 16 Thyr_Ag_Down Thyr_Ag_Down Inf 3.766883e-189 69
## 17 Ret_Ag_Up Thyr_Ag_Down 1.2697431 2.819577e-01 11
## 18 Ret_Ag_Down Thyr_Ag_Down 13.3903265 2.579072e-22 36
## 19 Estr_Ag_Up Thyr_Ag_Down 0.0000000 1.000000e+00 0
## 20 Estr_Ag_Down Thyr_Ag_Down 419.5878999 6.857653e-05 2
## 21 Andr_Ag_Up Thyr_Ag_Down 3.2895301 6.965485e-02 3
## 22 Andr_Ag_Down Thyr_Ag_Down 9.8466778 1.986370e-02 2
## 23 GC_Ag_Up Thyr_Ag_Down 0.0000000 1.000000e+00 0
## 24 GC_Ag_Down Thyr_Ag_Down 38.5053671 1.728186e-03 2
## 25 LivX_Ag_Up Thyr_Ag_Down 0.0000000 1.000000e+00 0
## 26 LivX_Ag_Down Thyr_Ag_Down 41.7418977 2.859911e-02 1
## 27 AhHyd_Ag_Up Thyr_Ag_Down 10.9979777 9.223306e-02 1
## 28 AhHyd_Ag_Down Thyr_Ag_Down 21.6994936 7.114372e-06 5
## 29 Thyr_Ag_Up Ret_Ag_Up 10.9510459 1.137907e-23 48
## 30 Thyr_Ag_Down Ret_Ag_Up 1.2697431 2.819577e-01 11
## 31 Ret_Ag_Up Ret_Ag_Up Inf 0.000000e+00 1861
## 32 Ret_Ag_Down Ret_Ag_Up 0.0000000 1.000000e+00 0
## 33 Estr_Ag_Up Ret_Ag_Up Inf 1.300944e-01 1
## 34 Estr_Ag_Down Ret_Ag_Up 3.3442545 3.417319e-01 1
## 35 Andr_Ag_Up Ret_Ag_Up 2.8474388 8.016126e-10 58
## 36 Andr_Ag_Down Ret_Ag_Up 3.7124461 9.868927e-05 16
## 37 GC_Ag_Up Ret_Ag_Up 13.3957228 3.442533e-03 4
## 38 GC_Ag_Down Ret_Ag_Up 2.9758029 7.772264e-02 4
## 39 LivX_Ag_Up Ret_Ag_Up 1.6723256 3.807545e-01 2
## 40 LivX_Ag_Down Ret_Ag_Up 13.3957228 3.442533e-03 4
## 41 AhHyd_Ag_Up Ret_Ag_Up 0.7427073 7.544395e-01 2
## 42 AhHyd_Ag_Down Ret_Ag_Up 7.8218662 4.642748e-13 30
## 43 Thyr_Ag_Up Ret_Ag_Down 3.3550283 7.805123e-05 17
## 44 Thyr_Ag_Down Ret_Ag_Down 13.3903265 2.579072e-22 36
## 45 Ret_Ag_Up Ret_Ag_Down 0.0000000 1.000000e+00 0
## 46 Ret_Ag_Down Ret_Ag_Down Inf 0.000000e+00 1108
## 47 Estr_Ag_Up Ret_Ag_Down 0.0000000 1.000000e+00 0
## 48 Estr_Ag_Down Ret_Ag_Down 0.0000000 1.000000e+00 0
## 49 Andr_Ag_Up Ret_Ag_Down 0.4352635 9.951476e-01 7
## 50 Andr_Ag_Down Ret_Ag_Down 1.4909839 2.675348e-01 5
## 51 GC_Ag_Up Ret_Ag_Down 0.0000000 1.000000e+00 0
## 52 GC_Ag_Down Ret_Ag_Down 0.9925479 6.495414e-01 1
## 53 LivX_Ag_Up Ret_Ag_Down 0.0000000 1.000000e+00 0
## 54 LivX_Ag_Down Ret_Ag_Down 0.0000000 1.000000e+00 0
## 55 AhHyd_Ag_Up Ret_Ag_Down 9.8136457 7.453704e-06 9
## 56 AhHyd_Ag_Down Ret_Ag_Down 3.2725273 1.007141e-03 12
## 57 Thyr_Ag_Up Estr_Ag_Up Inf 5.452639e-03 1
## 58 Thyr_Ag_Down Estr_Ag_Up 0.0000000 1.000000e+00 0
## 59 Ret_Ag_Up Estr_Ag_Up Inf 1.300944e-01 1
## 60 Ret_Ag_Down Estr_Ag_Up 0.0000000 1.000000e+00 0
## 61 Estr_Ag_Up Estr_Ag_Up Inf 6.990563e-05 1
## 62 Estr_Ag_Down Estr_Ag_Up 0.0000000 1.000000e+00 0
## 63 Andr_Ag_Up Estr_Ag_Up Inf 1.377141e-02 1
## 64 Andr_Ag_Down Estr_Ag_Up 0.0000000 1.000000e+00 0
## 65 GC_Ag_Up Estr_Ag_Up Inf 4.194338e-04 1
## 66 GC_Ag_Down Estr_Ag_Up 0.0000000 1.000000e+00 0
## 67 LivX_Ag_Up Estr_Ag_Up Inf 6.990563e-04 1
## 68 LivX_Ag_Down Estr_Ag_Up 0.0000000 1.000000e+00 0
## 69 AhHyd_Ag_Up Estr_Ag_Up Inf 1.398113e-03 1
## 70 AhHyd_Ag_Down Estr_Ag_Up 0.0000000 1.000000e+00 0
## 71 Thyr_Ag_Up Estr_Ag_Down 0.0000000 1.000000e+00 0
## 72 Thyr_Ag_Down Estr_Ag_Down 419.5878999 6.857653e-05 2
## 73 Ret_Ag_Up Estr_Ag_Down 3.3442545 3.417319e-01 1
## 74 Ret_Ag_Down Estr_Ag_Down 0.0000000 1.000000e+00 0
## 75 Estr_Ag_Up Estr_Ag_Down 0.0000000 1.000000e+00 0
## 76 Estr_Ag_Down Estr_Ag_Down Inf 2.050117e-12 3
## 77 Andr_Ag_Up Estr_Ag_Down 143.8041372 5.609612e-04 2
## 78 Andr_Ag_Down Estr_Ag_Down 0.0000000 1.000000e+00 0
## 79 GC_Ag_Up Estr_Ag_Down 0.0000000 1.000000e+00 0
## 80 GC_Ag_Down Estr_Ag_Down 572.4231226 2.724033e-03 1
## 81 LivX_Ag_Up Estr_Ag_Down 0.0000000 1.000000e+00 0
## 82 LivX_Ag_Down Estr_Ag_Down 1380.2902407 1.257861e-03 1
## 83 AhHyd_Ag_Up Estr_Ag_Down 0.0000000 1.000000e+00 0
## 84 AhHyd_Ag_Down Estr_Ag_Down 0.0000000 1.000000e+00 0
## 85 Thyr_Ag_Up Andr_Ag_Up 2.8929860 9.265938e-02 3
## 86 Thyr_Ag_Down Andr_Ag_Up 3.2895301 6.965485e-02 3
## 87 Ret_Ag_Up Andr_Ag_Up 2.8474388 8.016126e-10 58
## 88 Ret_Ag_Down Andr_Ag_Up 0.4352635 9.951476e-01 7
## 89 Estr_Ag_Up Andr_Ag_Up Inf 1.377141e-02 1
## 90 Estr_Ag_Down Andr_Ag_Up 143.8041372 5.609612e-04 2
## 91 Andr_Ag_Up Andr_Ag_Up Inf 0.000000e+00 197
## 92 Andr_Ag_Down Andr_Ag_Up 0.0000000 1.000000e+00 0
## 93 GC_Ag_Up Andr_Ag_Up 72.5837635 4.989996e-05 3
## 94 GC_Ag_Down Andr_Ag_Up 45.8103110 5.539904e-07 5
## 95 LivX_Ag_Up Andr_Ag_Up 7.9892731 1.295240e-01 1
## 96 LivX_Ag_Down Andr_Ag_Up 36.1085325 2.729185e-03 2
## 97 AhHyd_Ag_Up Andr_Ag_Up 12.8099630 2.467071e-03 3
## 98 AhHyd_Ag_Down Andr_Ag_Up 0.0000000 1.000000e+00 0
## 99 Thyr_Ag_Up Andr_Ag_Down 0.0000000 1.000000e+00 0
## 100 Thyr_Ag_Down Andr_Ag_Down 9.8466778 1.986370e-02 2
## 101 Ret_Ag_Up Andr_Ag_Down 3.7124461 9.868927e-05 16
## 102 Ret_Ag_Down Andr_Ag_Down 1.4909839 2.675348e-01 5
## 103 Estr_Ag_Up Andr_Ag_Down 0.0000000 1.000000e+00 0
## 104 Estr_Ag_Down Andr_Ag_Down 0.0000000 1.000000e+00 0
## 105 Andr_Ag_Up Andr_Ag_Down 0.0000000 1.000000e+00 0
## 106 Andr_Ag_Down Andr_Ag_Down Inf 1.291057e-131 45
## 107 GC_Ag_Up Andr_Ag_Down 0.0000000 1.000000e+00 0
## 108 GC_Ag_Down Andr_Ag_Down 26.9525489 4.014828e-02 1
## 109 LivX_Ag_Up Andr_Ag_Down 0.0000000 1.000000e+00 0
## 110 LivX_Ag_Down Andr_Ag_Down 0.0000000 1.000000e+00 0
## 111 AhHyd_Ag_Up Andr_Ag_Down 0.0000000 1.000000e+00 0
## 112 AhHyd_Ag_Down Andr_Ag_Down 12.2268934 1.337955e-02 2
## 113 Thyr_Ag_Up GC_Ag_Up 36.8350164 3.227866e-02 1
## 114 Thyr_Ag_Down GC_Ag_Up 0.0000000 1.000000e+00 0
## 115 Ret_Ag_Up GC_Ag_Up 13.3957228 3.442533e-03 4
## 116 Ret_Ag_Down GC_Ag_Up 0.0000000 1.000000e+00 0
## 117 Estr_Ag_Up GC_Ag_Up Inf 4.194338e-04 1
## 118 Estr_Ag_Down GC_Ag_Up 0.0000000 1.000000e+00 0
## 119 Andr_Ag_Up GC_Ag_Up 72.5837635 4.989996e-05 3
## 120 Andr_Ag_Down GC_Ag_Up 0.0000000 1.000000e+00 0
## 121 GC_Ag_Up GC_Ag_Up Inf 8.411255e-23 6
## 122 GC_Ag_Down GC_Ag_Up 0.0000000 1.000000e+00 0
## 123 LivX_Ag_Up GC_Ag_Up 315.8151426 4.187745e-03 1
## 124 LivX_Ag_Down GC_Ag_Up 0.0000000 1.000000e+00 0
## 125 AhHyd_Ag_Up GC_Ag_Up 148.9901154 8.360865e-03 1
## 126 AhHyd_Ag_Down GC_Ag_Up 0.0000000 1.000000e+00 0
## 127 Thyr_Ag_Up GC_Ag_Down 0.0000000 1.000000e+00 0
## 128 Thyr_Ag_Down GC_Ag_Down 38.5053671 1.728186e-03 2
## 129 Ret_Ag_Up GC_Ag_Down 2.9758029 7.772264e-02 4
## 130 Ret_Ag_Down GC_Ag_Down 0.9925479 6.495414e-01 1
## 131 Estr_Ag_Up GC_Ag_Down 0.0000000 1.000000e+00 0
## 132 Estr_Ag_Down GC_Ag_Down 572.4231226 2.724033e-03 1
## 133 Andr_Ag_Up GC_Ag_Down 45.8103110 5.539904e-07 5
## 134 Andr_Ag_Down GC_Ag_Down 26.9525489 4.014828e-02 1
## 135 GC_Ag_Up GC_Ag_Down 0.0000000 1.000000e+00 0
## 136 GC_Ag_Down GC_Ag_Down Inf 5.960832e-45 13
## 137 LivX_Ag_Up GC_Ag_Down 0.0000000 1.000000e+00 0
## 138 LivX_Ag_Down GC_Ag_Down 1338.8541918 1.170823e-08 3
## 139 AhHyd_Ag_Up GC_Ag_Down 0.0000000 1.000000e+00 0
## 140 AhHyd_Ag_Down GC_Ag_Down 0.0000000 1.000000e+00 0
## 141 Thyr_Ag_Up LivX_Ag_Up 20.5018984 5.322409e-02 1
## 142 Thyr_Ag_Down LivX_Ag_Up 0.0000000 1.000000e+00 0
## 143 Ret_Ag_Up LivX_Ag_Up 1.6723256 3.807545e-01 2
## 144 Ret_Ag_Down LivX_Ag_Up 0.0000000 1.000000e+00 0
## 145 Estr_Ag_Up LivX_Ag_Up Inf 6.990563e-04 1
## 146 Estr_Ag_Down LivX_Ag_Up 0.0000000 1.000000e+00 0
## 147 Andr_Ag_Up LivX_Ag_Up 7.9892731 1.295240e-01 1
## 148 Andr_Ag_Down LivX_Ag_Up 0.0000000 1.000000e+00 0
## 149 GC_Ag_Up LivX_Ag_Up 315.8151426 4.187745e-03 1
## 150 GC_Ag_Down LivX_Ag_Up 0.0000000 1.000000e+00 0
## 151 LivX_Ag_Up LivX_Ag_Up Inf 1.014497e-35 10
## 152 LivX_Ag_Down LivX_Ag_Up 0.0000000 1.000000e+00 0
## 153 AhHyd_Ag_Up LivX_Ag_Up 83.1198722 1.389784e-02 1
## 154 AhHyd_Ag_Down LivX_Ag_Up 0.0000000 1.000000e+00 0
## 155 Thyr_Ag_Up LivX_Ag_Down 36.8350164 3.227866e-02 1
## 156 Thyr_Ag_Down LivX_Ag_Down 41.7418977 2.859911e-02 1
## 157 Ret_Ag_Up LivX_Ag_Down 13.3957228 3.442533e-03 4
## 158 Ret_Ag_Down LivX_Ag_Down 0.0000000 1.000000e+00 0
## 159 Estr_Ag_Up LivX_Ag_Down 0.0000000 1.000000e+00 0
## 160 Estr_Ag_Down LivX_Ag_Down 1380.2902407 1.257861e-03 1
## 161 Andr_Ag_Up LivX_Ag_Down 36.1085325 2.729185e-03 2
## 162 Andr_Ag_Down LivX_Ag_Down 0.0000000 1.000000e+00 0
## 163 GC_Ag_Up LivX_Ag_Down 0.0000000 1.000000e+00 0
## 164 GC_Ag_Down LivX_Ag_Down 1338.8541918 1.170823e-08 3
## 165 LivX_Ag_Up LivX_Ag_Down 0.0000000 1.000000e+00 0
## 166 LivX_Ag_Down LivX_Ag_Down Inf 8.411255e-23 6
## 167 AhHyd_Ag_Up LivX_Ag_Down 0.0000000 1.000000e+00 0
## 168 AhHyd_Ag_Down LivX_Ag_Down 0.0000000 1.000000e+00 0
## 169 Thyr_Ag_Up AhHyd_Ag_Up 20.7363905 5.232939e-03 2
## 170 Thyr_Ag_Down AhHyd_Ag_Up 10.9979777 9.223306e-02 1
## 171 Ret_Ag_Up AhHyd_Ag_Up 0.7427073 7.544395e-01 2
## 172 Ret_Ag_Down AhHyd_Ag_Up 9.8136457 7.453704e-06 9
## 173 Estr_Ag_Up AhHyd_Ag_Up Inf 1.398113e-03 1
## 174 Estr_Ag_Down AhHyd_Ag_Up 0.0000000 1.000000e+00 0
## 175 Andr_Ag_Up AhHyd_Ag_Up 12.8099630 2.467071e-03 3
## 176 Andr_Ag_Down AhHyd_Ag_Up 0.0000000 1.000000e+00 0
## 177 GC_Ag_Up AhHyd_Ag_Up 148.9901154 8.360865e-03 1
## 178 GC_Ag_Down AhHyd_Ag_Up 0.0000000 1.000000e+00 0
## 179 LivX_Ag_Up AhHyd_Ag_Up 83.1198722 1.389784e-02 1
## 180 LivX_Ag_Down AhHyd_Ag_Up 0.0000000 1.000000e+00 0
## 181 AhHyd_Ag_Up AhHyd_Ag_Up Inf 1.914866e-65 20
## 182 AhHyd_Ag_Down AhHyd_Ag_Up 0.0000000 1.000000e+00 0
## 183 Thyr_Ag_Up AhHyd_Ag_Down 6.9029478 3.739553e-02 2
## 184 Thyr_Ag_Down AhHyd_Ag_Down 21.6994936 7.114372e-06 5
## 185 Ret_Ag_Up AhHyd_Ag_Down 7.8218662 4.642748e-13 30
## 186 Ret_Ag_Down AhHyd_Ag_Down 3.2725273 1.007141e-03 12
## 187 Estr_Ag_Up AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 188 Estr_Ag_Down AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 189 Andr_Ag_Up AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 190 Andr_Ag_Down AhHyd_Ag_Down 12.2268934 1.337955e-02 2
## 191 GC_Ag_Up AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 192 GC_Ag_Down AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 193 LivX_Ag_Up AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 194 LivX_Ag_Down AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 195 AhHyd_Ag_Up AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 196 AhHyd_Ag_Down AhHyd_Ag_Down Inf 1.553685e-158 56
<- Res
ResMod
$DEGs == ResMod$KBase, ]$OR <- 1
ResMod[ResMod$DEGs == ResMod$KBase, ]$Pval <- 1
ResMod[ResMod
ResMod## DEGs KBase OR Pval Numbers
## 1 Thyr_Ag_Up Thyr_Ag_Up 1.0000000 1.000000e+00 78
## 2 Thyr_Ag_Down Thyr_Ag_Up 0.0000000 1.000000e+00 0
## 3 Ret_Ag_Up Thyr_Ag_Up 10.9510459 1.137907e-23 48
## 4 Ret_Ag_Down Thyr_Ag_Up 3.3550283 7.805123e-05 17
## 5 Estr_Ag_Up Thyr_Ag_Up Inf 5.452639e-03 1
## 6 Estr_Ag_Down Thyr_Ag_Up 0.0000000 1.000000e+00 0
## 7 Andr_Ag_Up Thyr_Ag_Up 2.8929860 9.265938e-02 3
## 8 Andr_Ag_Down Thyr_Ag_Up 0.0000000 1.000000e+00 0
## 9 GC_Ag_Up Thyr_Ag_Up 36.8350164 3.227866e-02 1
## 10 GC_Ag_Down Thyr_Ag_Up 0.0000000 1.000000e+00 0
## 11 LivX_Ag_Up Thyr_Ag_Up 20.5018984 5.322409e-02 1
## 12 LivX_Ag_Down Thyr_Ag_Up 36.8350164 3.227866e-02 1
## 13 AhHyd_Ag_Up Thyr_Ag_Up 20.7363905 5.232939e-03 2
## 14 AhHyd_Ag_Down Thyr_Ag_Up 6.9029478 3.739553e-02 2
## 15 Thyr_Ag_Up Thyr_Ag_Down 0.0000000 1.000000e+00 0
## 16 Thyr_Ag_Down Thyr_Ag_Down 1.0000000 1.000000e+00 69
## 17 Ret_Ag_Up Thyr_Ag_Down 1.2697431 2.819577e-01 11
## 18 Ret_Ag_Down Thyr_Ag_Down 13.3903265 2.579072e-22 36
## 19 Estr_Ag_Up Thyr_Ag_Down 0.0000000 1.000000e+00 0
## 20 Estr_Ag_Down Thyr_Ag_Down 419.5878999 6.857653e-05 2
## 21 Andr_Ag_Up Thyr_Ag_Down 3.2895301 6.965485e-02 3
## 22 Andr_Ag_Down Thyr_Ag_Down 9.8466778 1.986370e-02 2
## 23 GC_Ag_Up Thyr_Ag_Down 0.0000000 1.000000e+00 0
## 24 GC_Ag_Down Thyr_Ag_Down 38.5053671 1.728186e-03 2
## 25 LivX_Ag_Up Thyr_Ag_Down 0.0000000 1.000000e+00 0
## 26 LivX_Ag_Down Thyr_Ag_Down 41.7418977 2.859911e-02 1
## 27 AhHyd_Ag_Up Thyr_Ag_Down 10.9979777 9.223306e-02 1
## 28 AhHyd_Ag_Down Thyr_Ag_Down 21.6994936 7.114372e-06 5
## 29 Thyr_Ag_Up Ret_Ag_Up 10.9510459 1.137907e-23 48
## 30 Thyr_Ag_Down Ret_Ag_Up 1.2697431 2.819577e-01 11
## 31 Ret_Ag_Up Ret_Ag_Up 1.0000000 1.000000e+00 1861
## 32 Ret_Ag_Down Ret_Ag_Up 0.0000000 1.000000e+00 0
## 33 Estr_Ag_Up Ret_Ag_Up Inf 1.300944e-01 1
## 34 Estr_Ag_Down Ret_Ag_Up 3.3442545 3.417319e-01 1
## 35 Andr_Ag_Up Ret_Ag_Up 2.8474388 8.016126e-10 58
## 36 Andr_Ag_Down Ret_Ag_Up 3.7124461 9.868927e-05 16
## 37 GC_Ag_Up Ret_Ag_Up 13.3957228 3.442533e-03 4
## 38 GC_Ag_Down Ret_Ag_Up 2.9758029 7.772264e-02 4
## 39 LivX_Ag_Up Ret_Ag_Up 1.6723256 3.807545e-01 2
## 40 LivX_Ag_Down Ret_Ag_Up 13.3957228 3.442533e-03 4
## 41 AhHyd_Ag_Up Ret_Ag_Up 0.7427073 7.544395e-01 2
## 42 AhHyd_Ag_Down Ret_Ag_Up 7.8218662 4.642748e-13 30
## 43 Thyr_Ag_Up Ret_Ag_Down 3.3550283 7.805123e-05 17
## 44 Thyr_Ag_Down Ret_Ag_Down 13.3903265 2.579072e-22 36
## 45 Ret_Ag_Up Ret_Ag_Down 0.0000000 1.000000e+00 0
## 46 Ret_Ag_Down Ret_Ag_Down 1.0000000 1.000000e+00 1108
## 47 Estr_Ag_Up Ret_Ag_Down 0.0000000 1.000000e+00 0
## 48 Estr_Ag_Down Ret_Ag_Down 0.0000000 1.000000e+00 0
## 49 Andr_Ag_Up Ret_Ag_Down 0.4352635 9.951476e-01 7
## 50 Andr_Ag_Down Ret_Ag_Down 1.4909839 2.675348e-01 5
## 51 GC_Ag_Up Ret_Ag_Down 0.0000000 1.000000e+00 0
## 52 GC_Ag_Down Ret_Ag_Down 0.9925479 6.495414e-01 1
## 53 LivX_Ag_Up Ret_Ag_Down 0.0000000 1.000000e+00 0
## 54 LivX_Ag_Down Ret_Ag_Down 0.0000000 1.000000e+00 0
## 55 AhHyd_Ag_Up Ret_Ag_Down 9.8136457 7.453704e-06 9
## 56 AhHyd_Ag_Down Ret_Ag_Down 3.2725273 1.007141e-03 12
## 57 Thyr_Ag_Up Estr_Ag_Up Inf 5.452639e-03 1
## 58 Thyr_Ag_Down Estr_Ag_Up 0.0000000 1.000000e+00 0
## 59 Ret_Ag_Up Estr_Ag_Up Inf 1.300944e-01 1
## 60 Ret_Ag_Down Estr_Ag_Up 0.0000000 1.000000e+00 0
## 61 Estr_Ag_Up Estr_Ag_Up 1.0000000 1.000000e+00 1
## 62 Estr_Ag_Down Estr_Ag_Up 0.0000000 1.000000e+00 0
## 63 Andr_Ag_Up Estr_Ag_Up Inf 1.377141e-02 1
## 64 Andr_Ag_Down Estr_Ag_Up 0.0000000 1.000000e+00 0
## 65 GC_Ag_Up Estr_Ag_Up Inf 4.194338e-04 1
## 66 GC_Ag_Down Estr_Ag_Up 0.0000000 1.000000e+00 0
## 67 LivX_Ag_Up Estr_Ag_Up Inf 6.990563e-04 1
## 68 LivX_Ag_Down Estr_Ag_Up 0.0000000 1.000000e+00 0
## 69 AhHyd_Ag_Up Estr_Ag_Up Inf 1.398113e-03 1
## 70 AhHyd_Ag_Down Estr_Ag_Up 0.0000000 1.000000e+00 0
## 71 Thyr_Ag_Up Estr_Ag_Down 0.0000000 1.000000e+00 0
## 72 Thyr_Ag_Down Estr_Ag_Down 419.5878999 6.857653e-05 2
## 73 Ret_Ag_Up Estr_Ag_Down 3.3442545 3.417319e-01 1
## 74 Ret_Ag_Down Estr_Ag_Down 0.0000000 1.000000e+00 0
## 75 Estr_Ag_Up Estr_Ag_Down 0.0000000 1.000000e+00 0
## 76 Estr_Ag_Down Estr_Ag_Down 1.0000000 1.000000e+00 3
## 77 Andr_Ag_Up Estr_Ag_Down 143.8041372 5.609612e-04 2
## 78 Andr_Ag_Down Estr_Ag_Down 0.0000000 1.000000e+00 0
## 79 GC_Ag_Up Estr_Ag_Down 0.0000000 1.000000e+00 0
## 80 GC_Ag_Down Estr_Ag_Down 572.4231226 2.724033e-03 1
## 81 LivX_Ag_Up Estr_Ag_Down 0.0000000 1.000000e+00 0
## 82 LivX_Ag_Down Estr_Ag_Down 1380.2902407 1.257861e-03 1
## 83 AhHyd_Ag_Up Estr_Ag_Down 0.0000000 1.000000e+00 0
## 84 AhHyd_Ag_Down Estr_Ag_Down 0.0000000 1.000000e+00 0
## 85 Thyr_Ag_Up Andr_Ag_Up 2.8929860 9.265938e-02 3
## 86 Thyr_Ag_Down Andr_Ag_Up 3.2895301 6.965485e-02 3
## 87 Ret_Ag_Up Andr_Ag_Up 2.8474388 8.016126e-10 58
## 88 Ret_Ag_Down Andr_Ag_Up 0.4352635 9.951476e-01 7
## 89 Estr_Ag_Up Andr_Ag_Up Inf 1.377141e-02 1
## 90 Estr_Ag_Down Andr_Ag_Up 143.8041372 5.609612e-04 2
## 91 Andr_Ag_Up Andr_Ag_Up 1.0000000 1.000000e+00 197
## 92 Andr_Ag_Down Andr_Ag_Up 0.0000000 1.000000e+00 0
## 93 GC_Ag_Up Andr_Ag_Up 72.5837635 4.989996e-05 3
## 94 GC_Ag_Down Andr_Ag_Up 45.8103110 5.539904e-07 5
## 95 LivX_Ag_Up Andr_Ag_Up 7.9892731 1.295240e-01 1
## 96 LivX_Ag_Down Andr_Ag_Up 36.1085325 2.729185e-03 2
## 97 AhHyd_Ag_Up Andr_Ag_Up 12.8099630 2.467071e-03 3
## 98 AhHyd_Ag_Down Andr_Ag_Up 0.0000000 1.000000e+00 0
## 99 Thyr_Ag_Up Andr_Ag_Down 0.0000000 1.000000e+00 0
## 100 Thyr_Ag_Down Andr_Ag_Down 9.8466778 1.986370e-02 2
## 101 Ret_Ag_Up Andr_Ag_Down 3.7124461 9.868927e-05 16
## 102 Ret_Ag_Down Andr_Ag_Down 1.4909839 2.675348e-01 5
## 103 Estr_Ag_Up Andr_Ag_Down 0.0000000 1.000000e+00 0
## 104 Estr_Ag_Down Andr_Ag_Down 0.0000000 1.000000e+00 0
## 105 Andr_Ag_Up Andr_Ag_Down 0.0000000 1.000000e+00 0
## 106 Andr_Ag_Down Andr_Ag_Down 1.0000000 1.000000e+00 45
## 107 GC_Ag_Up Andr_Ag_Down 0.0000000 1.000000e+00 0
## 108 GC_Ag_Down Andr_Ag_Down 26.9525489 4.014828e-02 1
## 109 LivX_Ag_Up Andr_Ag_Down 0.0000000 1.000000e+00 0
## 110 LivX_Ag_Down Andr_Ag_Down 0.0000000 1.000000e+00 0
## 111 AhHyd_Ag_Up Andr_Ag_Down 0.0000000 1.000000e+00 0
## 112 AhHyd_Ag_Down Andr_Ag_Down 12.2268934 1.337955e-02 2
## 113 Thyr_Ag_Up GC_Ag_Up 36.8350164 3.227866e-02 1
## 114 Thyr_Ag_Down GC_Ag_Up 0.0000000 1.000000e+00 0
## 115 Ret_Ag_Up GC_Ag_Up 13.3957228 3.442533e-03 4
## 116 Ret_Ag_Down GC_Ag_Up 0.0000000 1.000000e+00 0
## 117 Estr_Ag_Up GC_Ag_Up Inf 4.194338e-04 1
## 118 Estr_Ag_Down GC_Ag_Up 0.0000000 1.000000e+00 0
## 119 Andr_Ag_Up GC_Ag_Up 72.5837635 4.989996e-05 3
## 120 Andr_Ag_Down GC_Ag_Up 0.0000000 1.000000e+00 0
## 121 GC_Ag_Up GC_Ag_Up 1.0000000 1.000000e+00 6
## 122 GC_Ag_Down GC_Ag_Up 0.0000000 1.000000e+00 0
## 123 LivX_Ag_Up GC_Ag_Up 315.8151426 4.187745e-03 1
## 124 LivX_Ag_Down GC_Ag_Up 0.0000000 1.000000e+00 0
## 125 AhHyd_Ag_Up GC_Ag_Up 148.9901154 8.360865e-03 1
## 126 AhHyd_Ag_Down GC_Ag_Up 0.0000000 1.000000e+00 0
## 127 Thyr_Ag_Up GC_Ag_Down 0.0000000 1.000000e+00 0
## 128 Thyr_Ag_Down GC_Ag_Down 38.5053671 1.728186e-03 2
## 129 Ret_Ag_Up GC_Ag_Down 2.9758029 7.772264e-02 4
## 130 Ret_Ag_Down GC_Ag_Down 0.9925479 6.495414e-01 1
## 131 Estr_Ag_Up GC_Ag_Down 0.0000000 1.000000e+00 0
## 132 Estr_Ag_Down GC_Ag_Down 572.4231226 2.724033e-03 1
## 133 Andr_Ag_Up GC_Ag_Down 45.8103110 5.539904e-07 5
## 134 Andr_Ag_Down GC_Ag_Down 26.9525489 4.014828e-02 1
## 135 GC_Ag_Up GC_Ag_Down 0.0000000 1.000000e+00 0
## 136 GC_Ag_Down GC_Ag_Down 1.0000000 1.000000e+00 13
## 137 LivX_Ag_Up GC_Ag_Down 0.0000000 1.000000e+00 0
## 138 LivX_Ag_Down GC_Ag_Down 1338.8541918 1.170823e-08 3
## 139 AhHyd_Ag_Up GC_Ag_Down 0.0000000 1.000000e+00 0
## 140 AhHyd_Ag_Down GC_Ag_Down 0.0000000 1.000000e+00 0
## 141 Thyr_Ag_Up LivX_Ag_Up 20.5018984 5.322409e-02 1
## 142 Thyr_Ag_Down LivX_Ag_Up 0.0000000 1.000000e+00 0
## 143 Ret_Ag_Up LivX_Ag_Up 1.6723256 3.807545e-01 2
## 144 Ret_Ag_Down LivX_Ag_Up 0.0000000 1.000000e+00 0
## 145 Estr_Ag_Up LivX_Ag_Up Inf 6.990563e-04 1
## 146 Estr_Ag_Down LivX_Ag_Up 0.0000000 1.000000e+00 0
## 147 Andr_Ag_Up LivX_Ag_Up 7.9892731 1.295240e-01 1
## 148 Andr_Ag_Down LivX_Ag_Up 0.0000000 1.000000e+00 0
## 149 GC_Ag_Up LivX_Ag_Up 315.8151426 4.187745e-03 1
## 150 GC_Ag_Down LivX_Ag_Up 0.0000000 1.000000e+00 0
## 151 LivX_Ag_Up LivX_Ag_Up 1.0000000 1.000000e+00 10
## 152 LivX_Ag_Down LivX_Ag_Up 0.0000000 1.000000e+00 0
## 153 AhHyd_Ag_Up LivX_Ag_Up 83.1198722 1.389784e-02 1
## 154 AhHyd_Ag_Down LivX_Ag_Up 0.0000000 1.000000e+00 0
## 155 Thyr_Ag_Up LivX_Ag_Down 36.8350164 3.227866e-02 1
## 156 Thyr_Ag_Down LivX_Ag_Down 41.7418977 2.859911e-02 1
## 157 Ret_Ag_Up LivX_Ag_Down 13.3957228 3.442533e-03 4
## 158 Ret_Ag_Down LivX_Ag_Down 0.0000000 1.000000e+00 0
## 159 Estr_Ag_Up LivX_Ag_Down 0.0000000 1.000000e+00 0
## 160 Estr_Ag_Down LivX_Ag_Down 1380.2902407 1.257861e-03 1
## 161 Andr_Ag_Up LivX_Ag_Down 36.1085325 2.729185e-03 2
## 162 Andr_Ag_Down LivX_Ag_Down 0.0000000 1.000000e+00 0
## 163 GC_Ag_Up LivX_Ag_Down 0.0000000 1.000000e+00 0
## 164 GC_Ag_Down LivX_Ag_Down 1338.8541918 1.170823e-08 3
## 165 LivX_Ag_Up LivX_Ag_Down 0.0000000 1.000000e+00 0
## 166 LivX_Ag_Down LivX_Ag_Down 1.0000000 1.000000e+00 6
## 167 AhHyd_Ag_Up LivX_Ag_Down 0.0000000 1.000000e+00 0
## 168 AhHyd_Ag_Down LivX_Ag_Down 0.0000000 1.000000e+00 0
## 169 Thyr_Ag_Up AhHyd_Ag_Up 20.7363905 5.232939e-03 2
## 170 Thyr_Ag_Down AhHyd_Ag_Up 10.9979777 9.223306e-02 1
## 171 Ret_Ag_Up AhHyd_Ag_Up 0.7427073 7.544395e-01 2
## 172 Ret_Ag_Down AhHyd_Ag_Up 9.8136457 7.453704e-06 9
## 173 Estr_Ag_Up AhHyd_Ag_Up Inf 1.398113e-03 1
## 174 Estr_Ag_Down AhHyd_Ag_Up 0.0000000 1.000000e+00 0
## 175 Andr_Ag_Up AhHyd_Ag_Up 12.8099630 2.467071e-03 3
## 176 Andr_Ag_Down AhHyd_Ag_Up 0.0000000 1.000000e+00 0
## 177 GC_Ag_Up AhHyd_Ag_Up 148.9901154 8.360865e-03 1
## 178 GC_Ag_Down AhHyd_Ag_Up 0.0000000 1.000000e+00 0
## 179 LivX_Ag_Up AhHyd_Ag_Up 83.1198722 1.389784e-02 1
## 180 LivX_Ag_Down AhHyd_Ag_Up 0.0000000 1.000000e+00 0
## 181 AhHyd_Ag_Up AhHyd_Ag_Up 1.0000000 1.000000e+00 20
## 182 AhHyd_Ag_Down AhHyd_Ag_Up 0.0000000 1.000000e+00 0
## 183 Thyr_Ag_Up AhHyd_Ag_Down 6.9029478 3.739553e-02 2
## 184 Thyr_Ag_Down AhHyd_Ag_Down 21.6994936 7.114372e-06 5
## 185 Ret_Ag_Up AhHyd_Ag_Down 7.8218662 4.642748e-13 30
## 186 Ret_Ag_Down AhHyd_Ag_Down 3.2725273 1.007141e-03 12
## 187 Estr_Ag_Up AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 188 Estr_Ag_Down AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 189 Andr_Ag_Up AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 190 Andr_Ag_Down AhHyd_Ag_Down 12.2268934 1.337955e-02 2
## 191 GC_Ag_Up AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 192 GC_Ag_Down AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 193 LivX_Ag_Up AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 194 LivX_Ag_Down AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 195 AhHyd_Ag_Up AhHyd_Ag_Down 0.0000000 1.000000e+00 0
## 196 AhHyd_Ag_Down AhHyd_Ag_Down 1.0000000 1.000000e+00 56
I select as significant overlaps having an OR > 2 and at least 25 overlapping genes. Dots are shown for PVals < 0.01 (set in the plot). Max value in the plot must be set according to minimum PVal to avoid dots not to be shown.
<- viridis::cividis(100)[1:80]
cols <- dplyr::filter(ResMod, OR > 2) %>% dplyr::filter(Numbers > 25)
ResSel min(ResSel$Pval)
## [1] 1.137907e-23
max(ResSel$OR)
## [1] 13.39033
<- ggplot(ResSel, aes(DEGs, KBase, label=Numbers)) +
Dot geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1)) +
ggtitle('Overlap across agonist-modulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_Agonist.pdf'), width=8, height=8)
<- c('Thyr_Ag_Up', 'Thyr_Ag_Down', 'Ret_Ag_Up', 'Ret_Ag_Down',
Path 'Estr_Ag_Up', 'Estr_Ag_Down', 'LivX_Ag_Up', 'LivX_Ag_Down')
<- ResSel[ResSel$DEGs %in% Path & ResSel$KBase %in% Path, ]
ResPath
ResPath## DEGs KBase OR Pval Numbers
## 1 Ret_Ag_Up Thyr_Ag_Up 10.95105 1.137907e-23 48
## 2 Ret_Ag_Down Thyr_Ag_Down 13.39033 2.579072e-22 36
## 3 Thyr_Ag_Up Ret_Ag_Up 10.95105 1.137907e-23 48
## 6 Thyr_Ag_Down Ret_Ag_Down 13.39033 2.579072e-22 36
<- dplyr::filter(ResPath, OR > 2) %>% dplyr::filter(Numbers > 25)
ResPath min(ResPath$Pval)
## [1] 1.137907e-23
max(ResPath$OR)
## [1] 13.39033
<- ggplot(ResPath, aes(DEGs, KBase, label=Numbers)) +
Dot geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1))+
ggtitle('Overlap across agonist-modulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_Agonist_Selected.pdf'), width=8, height=8)
<- list(
DEGs_Inh
Thyr_Inh_Up= row.names(DEA$Thyr$Inhibitor$DEGs[DEA$Thyr$Inhibitor$DEGs$log2FoldChange > 0, ]),
Thyr_Inh_Down= row.names(DEA$Thyr$Inhibitor$DEGs[DEA$Thyr$Inhibitor$DEGs$log2FoldChange < 0, ]),
Ret_Inh_Up= row.names(DEA$Ret$Inhibitor$DEGs[DEA$Ret$Inhibitor$DEGs$log2FoldChange > 0, ]),
Ret_Inh_Down= row.names(DEA$Ret$Inhibitor$DEGs[DEA$Ret$Inhibitor$DEGs$log2FoldChange < 0, ]),
Estr_Inh_Up= row.names(DEA$Estr$Inhibitor$DEGs[DEA$Estr$Inhibitor$DEGs$log2FoldChange > 0, ]),
Estr_Inh_Down= row.names(DEA$Estr$Inhibitor$DEGs[DEA$Estr$Inhibitor$DEGs$log2FoldChange < 0, ]),
Andr_Inh_Up= row.names(DEA$Andr$Inhibitor$DEGs[DEA$Andr$Inhibitor$DEGs$log2FoldChange > 0, ]),
Andr_Inh_Down= row.names(DEA$Andr$Inhibitor$DEGs[DEA$Andr$Inhibitor$DEGs$log2FoldChange < 0, ]),
GC_Inh_Up= row.names(DEA$GC$Inhibitor$DEGs[DEA$GC$Inhibitor$DEGs$log2FoldChange > 0, ]),
GC_Inh_Down= row.names(DEA$GC$Inhibitor$DEGs[DEA$GC$Inhibitor$DEGs$log2FoldChange < 0, ]),
LivX_Inh_Up= row.names(DEA$LivX$Inhibitor$DEGs[DEA$LivX$Inhibitor$DEGs$log2FoldChange > 0, ]),
LivX_Inh_Down= row.names(DEA$LivX$Inhibitor$DEGs[DEA$LivX$Inhibitor$DEGs$log2FoldChange < 0, ]),
AhHyd_Inh_Up= row.names(DEA$AhHyd$Inhibitor$DEGs[DEA$AhHyd$Inhibitor$DEGs$log2FoldChange > 0, ]),
AhHyd_Inh_Down= row.names(DEA$AhHyd$Inhibitor$DEGs[DEA$AhHyd$Inhibitor$DEGs$log2FoldChange < 0, ])
)
<- row.names(DEA$Ret$Inhibitor$Res) %>% unique()
Universe length(Universe)
## [1] 14305
<- newGOM(DEGs_Inh, DEGs_Inh, genome.size=length(Universe))
OvObj print(OvObj)
## A GeneOverlapMatrix object:
## ###### Intersection ######
## Thyr_Inh_Up Thyr_Inh_Down Ret_Inh_Up Ret_Inh_Down Estr_Inh_Up
## Thyr_Inh_Up 160 0 8 19 17
## Thyr_Inh_Down 0 257 14 12 0
## Ret_Inh_Up 8 14 147 0 5
## Ret_Inh_Down 19 12 0 640 4
## Estr_Inh_Up 17 0 5 4 26
## Estr_Inh_Down 0 36 0 10 0
## Andr_Inh_Up 2 0 2 0 2
## Andr_Inh_Down 1 12 0 4 0
## GC_Inh_Up 103 0 5 23 17
## GC_Inh_Down 0 177 24 10 1
## LivX_Inh_Up 107 0 6 24 18
## LivX_Inh_Down 0 135 23 7 2
## AhHyd_Inh_Up 22 6 11 48 4
## AhHyd_Inh_Down 8 57 2 16 0
## Estr_Inh_Down Andr_Inh_Up Andr_Inh_Down GC_Inh_Up GC_Inh_Down
## Thyr_Inh_Up 0 2 1 103 0
## Thyr_Inh_Down 36 0 12 0 177
## Ret_Inh_Up 0 2 0 5 24
## Ret_Inh_Down 10 0 4 23 10
## Estr_Inh_Up 0 2 0 17 1
## Estr_Inh_Down 56 0 8 0 39
## Andr_Inh_Up 0 11 0 3 0
## Andr_Inh_Down 8 0 20 0 11
## GC_Inh_Up 0 3 0 143 0
## GC_Inh_Down 39 0 11 0 294
## LivX_Inh_Up 0 3 0 93 0
## LivX_Inh_Down 26 0 9 0 155
## AhHyd_Inh_Up 3 8 0 27 8
## AhHyd_Inh_Down 17 0 15 5 57
## LivX_Inh_Up LivX_Inh_Down AhHyd_Inh_Up AhHyd_Inh_Down
## Thyr_Inh_Up 107 0 22 8
## Thyr_Inh_Down 0 135 6 57
## Ret_Inh_Up 6 23 11 2
## Ret_Inh_Down 24 7 48 16
## Estr_Inh_Up 18 2 4 0
## Estr_Inh_Down 0 26 3 17
## Andr_Inh_Up 3 0 8 0
## Andr_Inh_Down 0 9 0 15
## GC_Inh_Up 93 0 27 5
## GC_Inh_Down 0 155 8 57
## LivX_Inh_Up 149 0 18 7
## LivX_Inh_Down 0 202 9 39
## AhHyd_Inh_Up 18 9 229 0
## AhHyd_Inh_Down 7 39 0 134
## ###### P-value ######
## Thyr_Inh_Up Thyr_Inh_Down Ret_Inh_Up Ret_Inh_Down
## Thyr_Inh_Up 0.000000e+00 1.000000e+00 2.460360e-04 9.792842e-05
## Thyr_Inh_Down 1.000000e+00 0.000000e+00 4.071963e-07 4.818121e-01
## Ret_Inh_Up 2.460360e-04 4.071963e-07 0.000000e+00 1.000000e+00
## Ret_Inh_Down 9.792842e-05 4.818121e-01 1.000000e+00 0.000000e+00
## Estr_Inh_Up 8.053782e-28 1.000000e+00 5.916284e-06 2.711290e-02
## Estr_Inh_Down 1.000000e+00 6.684890e-50 1.000000e+00 1.652791e-04
## Andr_Inh_Up 6.399483e-03 1.000000e+00 5.428334e-03 1.000000e+00
## Andr_Inh_Down 2.015707e-01 9.704536e-17 1.000000e+00 1.084916e-02
## GC_Inh_Up 6.600656e-185 1.000000e+00 1.604266e-02 8.851576e-08
## GC_Inh_Down 1.000000e+00 4.525907e-261 3.003206e-15 8.527122e-01
## LivX_Inh_Up 7.156443e-193 1.000000e+00 4.384561e-03 4.516015e-08
## LivX_Inh_Down 1.000000e+00 7.883616e-201 7.649489e-18 8.047628e-01
## AhHyd_Inh_Up 9.863282e-15 2.304721e-01 2.439886e-05 1.193595e-19
## AhHyd_Inh_Down 1.300390e-04 4.969385e-65 4.014797e-01 3.196646e-04
## Estr_Inh_Up Estr_Inh_Down Andr_Inh_Up Andr_Inh_Down
## Thyr_Inh_Up 8.053782e-28 1.000000e+00 6.399483e-03 2.015707e-01
## Thyr_Inh_Down 1.000000e+00 6.684890e-50 1.000000e+00 9.704536e-17
## Ret_Inh_Up 5.916284e-06 1.000000e+00 5.428334e-03 1.000000e+00
## Ret_Inh_Down 2.711290e-02 1.652791e-04 1.000000e+00 1.084916e-02
## Estr_Inh_Up 3.739447e-82 1.000000e+00 1.729647e-04 1.000000e+00
## Estr_Inh_Down 1.000000e+00 1.553685e-158 1.000000e+00 3.977371e-15
## Andr_Inh_Up 1.729647e-04 1.000000e+00 7.806555e-39 1.000000e+00
## Andr_Inh_Down 1.000000e+00 3.977371e-15 1.000000e+00 1.914866e-65
## GC_Inh_Up 1.080777e-28 1.000000e+00 1.521924e-04 1.000000e+00
## GC_Inh_Down 4.174868e-01 8.701825e-54 1.000000e+00 3.269870e-14
## LivX_Inh_Up 1.052311e-30 1.000000e+00 1.718767e-04 1.000000e+00
## LivX_Inh_Down 5.165985e-02 6.967515e-34 1.000000e+00 2.742714e-12
## AhHyd_Inh_Up 7.250604e-04 6.045316e-02 6.045054e-13 1.000000e+00
## AhHyd_Inh_Down 1.000000e+00 8.339853e-22 1.000000e+00 2.497908e-27
## GC_Inh_Up GC_Inh_Down LivX_Inh_Up LivX_Inh_Down
## Thyr_Inh_Up 6.600656e-185 1.000000e+00 7.156443e-193 1.000000e+00
## Thyr_Inh_Down 1.000000e+00 4.525907e-261 1.000000e+00 7.883616e-201
## Ret_Inh_Up 1.604266e-02 3.003206e-15 4.384561e-03 7.649489e-18
## Ret_Inh_Down 8.851576e-08 8.527122e-01 4.516015e-08 8.047628e-01
## Estr_Inh_Up 1.080777e-28 4.174868e-01 1.052311e-30 5.165985e-02
## Estr_Inh_Down 1.000000e+00 8.701825e-54 1.000000e+00 6.967515e-34
## Andr_Inh_Up 1.521924e-04 1.000000e+00 1.718767e-04 1.000000e+00
## Andr_Inh_Down 1.000000e+00 3.269870e-14 1.000000e+00 2.742714e-12
## GC_Inh_Up 0.000000e+00 1.000000e+00 2.256262e-162 1.000000e+00
## GC_Inh_Down 1.000000e+00 0.000000e+00 1.000000e+00 1.370752e-237
## LivX_Inh_Up 2.256262e-162 1.000000e+00 0.000000e+00 1.000000e+00
## LivX_Inh_Down 1.000000e+00 1.370752e-237 1.000000e+00 0.000000e+00
## AhHyd_Inh_Up 1.443761e-21 1.006674e-01 2.683146e-11 5.291673e-03
## AhHyd_Inh_Down 1.110745e-02 2.156529e-61 5.032755e-04 4.722935e-41
## AhHyd_Inh_Up AhHyd_Inh_Down
## Thyr_Inh_Up 9.863282e-15 1.300390e-04
## Thyr_Inh_Down 2.304721e-01 4.969385e-65
## Ret_Inh_Up 2.439886e-05 4.014797e-01
## Ret_Inh_Down 1.193595e-19 3.196646e-04
## Estr_Inh_Up 7.250604e-04 1.000000e+00
## Estr_Inh_Down 6.045316e-02 8.339853e-22
## Andr_Inh_Up 6.045054e-13 1.000000e+00
## Andr_Inh_Down 1.000000e+00 2.497908e-27
## GC_Inh_Up 1.443761e-21 1.110745e-02
## GC_Inh_Down 1.006674e-01 2.156529e-61
## LivX_Inh_Up 2.683146e-11 5.032755e-04
## LivX_Inh_Down 5.291673e-03 4.722935e-41
## AhHyd_Inh_Up 0.000000e+00 1.000000e+00
## AhHyd_Inh_Down 1.000000e+00 0.000000e+00
## ###### Odds Ratio ######
## Thyr_Inh_Up Thyr_Inh_Down Ret_Inh_Up Ret_Inh_Down Estr_Inh_Up
## Thyr_Inh_Up Inf 0.000000 5.301812 2.9342197 185.216597
## Thyr_Inh_Down 0.000000 Inf 6.025815 1.0466803 0.000000
## Ret_Inh_Up 5.301812 6.025815 Inf 0.0000000 23.657303
## Ret_Inh_Down 2.934220 1.046680 0.000000 Inf 3.899834
## Estr_Inh_Up 185.216597 0.000000 23.657303 3.8998341 Inf
## Estr_Inh_Down 0.000000 113.747546 0.000000 4.6981515 0.000000
## Andr_Inh_Up 19.852088 0.000000 21.671062 0.0000000 131.212371
## Andr_Inh_Down 4.674573 85.721173 0.000000 5.3638099 0.000000
## GC_Inh_Up 643.982238 0.000000 3.577026 4.2068851 210.165381
## GC_Inh_Down 0.000000 261.728337 10.030152 0.7478817 1.909251
## LivX_Inh_Up 680.541601 0.000000 4.169265 4.2194779 241.447440
## LivX_Inh_Down 0.000000 229.219257 14.477847 0.7638911 5.864338
## AhHyd_Inh_Up 10.725756 1.481887 5.170198 6.0384071 11.349242
## AhHyd_Inh_Down 5.854020 51.576644 1.465541 2.9433413 0.000000
## Estr_Inh_Down Andr_Inh_Up Andr_Inh_Down GC_Inh_Up GC_Inh_Down
## Thyr_Inh_Up 0.000000 19.85209 4.674573 643.982238 0.0000000
## Thyr_Inh_Down 113.747546 0.00000 85.721173 0.000000 261.7283374
## Ret_Inh_Up 0.000000 21.67106 0.000000 3.577026 10.0301520
## Ret_Inh_Down 4.698151 0.00000 5.363810 4.206885 0.7478817
## Estr_Inh_Up 0.000000 131.21237 0.000000 210.165381 1.9092510
## Estr_Inh_Down Inf 0.00000 195.929068 0.000000 125.6235132
## Andr_Inh_Up 0.000000 Inf 0.000000 37.842924 0.0000000
## Andr_Inh_Down 195.929068 0.00000 Inf 0.000000 60.4186984
## GC_Inh_Up 0.000000 37.84292 0.000000 Inf 0.0000000
## GC_Inh_Down 125.623513 0.00000 60.418698 0.000000 Inf
## LivX_Inh_Up 0.000000 36.27646 0.000000 462.155024 0.0000000
## LivX_Inh_Down 69.118348 0.00000 59.590522 0.000000 328.9124164
## AhHyd_Inh_Up 3.511547 169.02939 0.000000 16.074371 1.7453123
## AhHyd_Inh_Down 52.500274 0.00000 353.654463 3.940650 43.4566049
## LivX_Inh_Up LivX_Inh_Down AhHyd_Inh_Up AhHyd_Inh_Down
## Thyr_Inh_Up 680.541601 0.0000000 10.725756 5.854020
## Thyr_Inh_Down 0.000000 229.2192571 1.481887 51.576644
## Ret_Inh_Up 4.169265 14.4778467 5.170198 1.465541
## Ret_Inh_Down 4.219478 0.7638911 6.038407 2.943341
## Estr_Inh_Up 241.447440 5.8643380 11.349242 0.000000
## Estr_Inh_Down 0.000000 69.1183483 3.511547 52.500274
## Andr_Inh_Up 36.276463 0.0000000 169.029389 0.000000
## Andr_Inh_Down 0.000000 59.5905220 0.000000 353.654463
## GC_Inh_Up 462.155024 0.0000000 16.074371 3.940650
## GC_Inh_Down 0.000000 328.9124164 1.745312 43.456605
## LivX_Inh_Up Inf 0.0000000 9.075724 5.444470
## LivX_Inh_Down 0.000000 Inf 2.942282 35.230183
## AhHyd_Inh_Up 9.075724 2.9422822 Inf 0.000000
## AhHyd_Inh_Down 5.444470 35.2301826 0.000000 Inf
## ###### Jaccard Index ######
## Thyr_Inh_Up Thyr_Inh_Down Ret_Inh_Up Ret_Inh_Down Estr_Inh_Up
## Thyr_Inh_Up 1.000000000 0.00000000 0.026755853 0.024327785 0.100591716
## Thyr_Inh_Down 0.000000000 1.00000000 0.035897436 0.013559322 0.000000000
## Ret_Inh_Up 0.026755853 0.03589744 1.000000000 0.000000000 0.029761905
## Ret_Inh_Down 0.024327785 0.01355932 0.000000000 1.000000000 0.006042296
## Estr_Inh_Up 0.100591716 0.00000000 0.029761905 0.006042296 1.000000000
## Estr_Inh_Down 0.000000000 0.12996390 0.000000000 0.014577259 0.000000000
## Andr_Inh_Up 0.011834320 0.00000000 0.012820513 0.000000000 0.057142857
## Andr_Inh_Down 0.005586592 0.04528302 0.000000000 0.006097561 0.000000000
## GC_Inh_Up 0.515000000 0.00000000 0.017543860 0.030263158 0.111842105
## GC_Inh_Down 0.000000000 0.47326203 0.057553957 0.010822511 0.003134796
## LivX_Inh_Up 0.529702970 0.00000000 0.020689655 0.031372549 0.114649682
## LivX_Inh_Down 0.000000000 0.41666667 0.070552147 0.008383234 0.008849558
## AhHyd_Inh_Up 0.059945504 0.01250000 0.030136986 0.058465286 0.015936255
## AhHyd_Inh_Down 0.027972028 0.17065868 0.007168459 0.021108179 0.000000000
## Estr_Inh_Down Andr_Inh_Up Andr_Inh_Down GC_Inh_Up GC_Inh_Down
## Thyr_Inh_Up 0.00000000 0.01183432 0.005586592 0.51500000 0.000000000
## Thyr_Inh_Down 0.12996390 0.00000000 0.045283019 0.00000000 0.473262032
## Ret_Inh_Up 0.00000000 0.01282051 0.000000000 0.01754386 0.057553957
## Ret_Inh_Down 0.01457726 0.00000000 0.006097561 0.03026316 0.010822511
## Estr_Inh_Up 0.00000000 0.05714286 0.000000000 0.11184211 0.003134796
## Estr_Inh_Down 1.00000000 0.00000000 0.117647059 0.00000000 0.125401929
## Andr_Inh_Up 0.00000000 1.00000000 0.000000000 0.01986755 0.000000000
## Andr_Inh_Down 0.11764706 0.00000000 1.000000000 0.00000000 0.036303630
## GC_Inh_Up 0.00000000 0.01986755 0.000000000 1.00000000 0.000000000
## GC_Inh_Down 0.12540193 0.00000000 0.036303630 0.00000000 1.000000000
## LivX_Inh_Up 0.00000000 0.01910828 0.000000000 0.46733668 0.000000000
## LivX_Inh_Down 0.11206897 0.00000000 0.042253521 0.00000000 0.454545455
## AhHyd_Inh_Up 0.01063830 0.03448276 0.000000000 0.07826087 0.015533981
## AhHyd_Inh_Down 0.09826590 0.00000000 0.107913669 0.01838235 0.153638814
## LivX_Inh_Up LivX_Inh_Down AhHyd_Inh_Up AhHyd_Inh_Down
## Thyr_Inh_Up 0.52970297 0.000000000 0.05994550 0.027972028
## Thyr_Inh_Down 0.00000000 0.416666667 0.01250000 0.170658683
## Ret_Inh_Up 0.02068966 0.070552147 0.03013699 0.007168459
## Ret_Inh_Down 0.03137255 0.008383234 0.05846529 0.021108179
## Estr_Inh_Up 0.11464968 0.008849558 0.01593625 0.000000000
## Estr_Inh_Down 0.00000000 0.112068966 0.01063830 0.098265896
## Andr_Inh_Up 0.01910828 0.000000000 0.03448276 0.000000000
## Andr_Inh_Down 0.00000000 0.042253521 0.00000000 0.107913669
## GC_Inh_Up 0.46733668 0.000000000 0.07826087 0.018382353
## GC_Inh_Down 0.00000000 0.454545455 0.01553398 0.153638814
## LivX_Inh_Up 1.00000000 0.000000000 0.05000000 0.025362319
## LivX_Inh_Down 0.00000000 1.000000000 0.02132701 0.131313131
## AhHyd_Inh_Up 0.05000000 0.021327014 1.00000000 0.000000000
## AhHyd_Inh_Down 0.02536232 0.131313131 0.00000000 1.000000000
getMatrix(OvObj, name='intersection')
## Thyr_Inh_Up Thyr_Inh_Down Ret_Inh_Up Ret_Inh_Down Estr_Inh_Up
## Thyr_Inh_Up 160 0 8 19 17
## Thyr_Inh_Down 0 257 14 12 0
## Ret_Inh_Up 8 14 147 0 5
## Ret_Inh_Down 19 12 0 640 4
## Estr_Inh_Up 17 0 5 4 26
## Estr_Inh_Down 0 36 0 10 0
## Andr_Inh_Up 2 0 2 0 2
## Andr_Inh_Down 1 12 0 4 0
## GC_Inh_Up 103 0 5 23 17
## GC_Inh_Down 0 177 24 10 1
## LivX_Inh_Up 107 0 6 24 18
## LivX_Inh_Down 0 135 23 7 2
## AhHyd_Inh_Up 22 6 11 48 4
## AhHyd_Inh_Down 8 57 2 16 0
## Estr_Inh_Down Andr_Inh_Up Andr_Inh_Down GC_Inh_Up GC_Inh_Down
## Thyr_Inh_Up 0 2 1 103 0
## Thyr_Inh_Down 36 0 12 0 177
## Ret_Inh_Up 0 2 0 5 24
## Ret_Inh_Down 10 0 4 23 10
## Estr_Inh_Up 0 2 0 17 1
## Estr_Inh_Down 56 0 8 0 39
## Andr_Inh_Up 0 11 0 3 0
## Andr_Inh_Down 8 0 20 0 11
## GC_Inh_Up 0 3 0 143 0
## GC_Inh_Down 39 0 11 0 294
## LivX_Inh_Up 0 3 0 93 0
## LivX_Inh_Down 26 0 9 0 155
## AhHyd_Inh_Up 3 8 0 27 8
## AhHyd_Inh_Down 17 0 15 5 57
## LivX_Inh_Up LivX_Inh_Down AhHyd_Inh_Up AhHyd_Inh_Down
## Thyr_Inh_Up 107 0 22 8
## Thyr_Inh_Down 0 135 6 57
## Ret_Inh_Up 6 23 11 2
## Ret_Inh_Down 24 7 48 16
## Estr_Inh_Up 18 2 4 0
## Estr_Inh_Down 0 26 3 17
## Andr_Inh_Up 3 0 8 0
## Andr_Inh_Down 0 9 0 15
## GC_Inh_Up 93 0 27 5
## GC_Inh_Down 0 155 8 57
## LivX_Inh_Up 149 0 18 7
## LivX_Inh_Down 0 202 9 39
## AhHyd_Inh_Up 18 9 229 0
## AhHyd_Inh_Down 7 39 0 134
getMatrix(OvObj, name='pval')
## Thyr_Inh_Up Thyr_Inh_Down Ret_Inh_Up Ret_Inh_Down
## Thyr_Inh_Up 0.000000e+00 1.000000e+00 2.460360e-04 9.792842e-05
## Thyr_Inh_Down 1.000000e+00 0.000000e+00 4.071963e-07 4.818121e-01
## Ret_Inh_Up 2.460360e-04 4.071963e-07 0.000000e+00 1.000000e+00
## Ret_Inh_Down 9.792842e-05 4.818121e-01 1.000000e+00 0.000000e+00
## Estr_Inh_Up 8.053782e-28 1.000000e+00 5.916284e-06 2.711290e-02
## Estr_Inh_Down 1.000000e+00 6.684890e-50 1.000000e+00 1.652791e-04
## Andr_Inh_Up 6.399483e-03 1.000000e+00 5.428334e-03 1.000000e+00
## Andr_Inh_Down 2.015707e-01 9.704536e-17 1.000000e+00 1.084916e-02
## GC_Inh_Up 6.600656e-185 1.000000e+00 1.604266e-02 8.851576e-08
## GC_Inh_Down 1.000000e+00 4.525907e-261 3.003206e-15 8.527122e-01
## LivX_Inh_Up 7.156443e-193 1.000000e+00 4.384561e-03 4.516015e-08
## LivX_Inh_Down 1.000000e+00 7.883616e-201 7.649489e-18 8.047628e-01
## AhHyd_Inh_Up 9.863282e-15 2.304721e-01 2.439886e-05 1.193595e-19
## AhHyd_Inh_Down 1.300390e-04 4.969385e-65 4.014797e-01 3.196646e-04
## Estr_Inh_Up Estr_Inh_Down Andr_Inh_Up Andr_Inh_Down
## Thyr_Inh_Up 8.053782e-28 1.000000e+00 6.399483e-03 2.015707e-01
## Thyr_Inh_Down 1.000000e+00 6.684890e-50 1.000000e+00 9.704536e-17
## Ret_Inh_Up 5.916284e-06 1.000000e+00 5.428334e-03 1.000000e+00
## Ret_Inh_Down 2.711290e-02 1.652791e-04 1.000000e+00 1.084916e-02
## Estr_Inh_Up 3.739447e-82 1.000000e+00 1.729647e-04 1.000000e+00
## Estr_Inh_Down 1.000000e+00 1.553685e-158 1.000000e+00 3.977371e-15
## Andr_Inh_Up 1.729647e-04 1.000000e+00 7.806555e-39 1.000000e+00
## Andr_Inh_Down 1.000000e+00 3.977371e-15 1.000000e+00 1.914866e-65
## GC_Inh_Up 1.080777e-28 1.000000e+00 1.521924e-04 1.000000e+00
## GC_Inh_Down 4.174868e-01 8.701825e-54 1.000000e+00 3.269870e-14
## LivX_Inh_Up 1.052311e-30 1.000000e+00 1.718767e-04 1.000000e+00
## LivX_Inh_Down 5.165985e-02 6.967515e-34 1.000000e+00 2.742714e-12
## AhHyd_Inh_Up 7.250604e-04 6.045316e-02 6.045054e-13 1.000000e+00
## AhHyd_Inh_Down 1.000000e+00 8.339853e-22 1.000000e+00 2.497908e-27
## GC_Inh_Up GC_Inh_Down LivX_Inh_Up LivX_Inh_Down
## Thyr_Inh_Up 6.600656e-185 1.000000e+00 7.156443e-193 1.000000e+00
## Thyr_Inh_Down 1.000000e+00 4.525907e-261 1.000000e+00 7.883616e-201
## Ret_Inh_Up 1.604266e-02 3.003206e-15 4.384561e-03 7.649489e-18
## Ret_Inh_Down 8.851576e-08 8.527122e-01 4.516015e-08 8.047628e-01
## Estr_Inh_Up 1.080777e-28 4.174868e-01 1.052311e-30 5.165985e-02
## Estr_Inh_Down 1.000000e+00 8.701825e-54 1.000000e+00 6.967515e-34
## Andr_Inh_Up 1.521924e-04 1.000000e+00 1.718767e-04 1.000000e+00
## Andr_Inh_Down 1.000000e+00 3.269870e-14 1.000000e+00 2.742714e-12
## GC_Inh_Up 0.000000e+00 1.000000e+00 2.256262e-162 1.000000e+00
## GC_Inh_Down 1.000000e+00 0.000000e+00 1.000000e+00 1.370752e-237
## LivX_Inh_Up 2.256262e-162 1.000000e+00 0.000000e+00 1.000000e+00
## LivX_Inh_Down 1.000000e+00 1.370752e-237 1.000000e+00 0.000000e+00
## AhHyd_Inh_Up 1.443761e-21 1.006674e-01 2.683146e-11 5.291673e-03
## AhHyd_Inh_Down 1.110745e-02 2.156529e-61 5.032755e-04 4.722935e-41
## AhHyd_Inh_Up AhHyd_Inh_Down
## Thyr_Inh_Up 9.863282e-15 1.300390e-04
## Thyr_Inh_Down 2.304721e-01 4.969385e-65
## Ret_Inh_Up 2.439886e-05 4.014797e-01
## Ret_Inh_Down 1.193595e-19 3.196646e-04
## Estr_Inh_Up 7.250604e-04 1.000000e+00
## Estr_Inh_Down 6.045316e-02 8.339853e-22
## Andr_Inh_Up 6.045054e-13 1.000000e+00
## Andr_Inh_Down 1.000000e+00 2.497908e-27
## GC_Inh_Up 1.443761e-21 1.110745e-02
## GC_Inh_Down 1.006674e-01 2.156529e-61
## LivX_Inh_Up 2.683146e-11 5.032755e-04
## LivX_Inh_Down 5.291673e-03 4.722935e-41
## AhHyd_Inh_Up 0.000000e+00 1.000000e+00
## AhHyd_Inh_Down 1.000000e+00 0.000000e+00
getMatrix(OvObj, name='odds.ratio')
## Thyr_Inh_Up Thyr_Inh_Down Ret_Inh_Up Ret_Inh_Down Estr_Inh_Up
## Thyr_Inh_Up Inf 0.000000 5.301812 2.9342197 185.216597
## Thyr_Inh_Down 0.000000 Inf 6.025815 1.0466803 0.000000
## Ret_Inh_Up 5.301812 6.025815 Inf 0.0000000 23.657303
## Ret_Inh_Down 2.934220 1.046680 0.000000 Inf 3.899834
## Estr_Inh_Up 185.216597 0.000000 23.657303 3.8998341 Inf
## Estr_Inh_Down 0.000000 113.747546 0.000000 4.6981515 0.000000
## Andr_Inh_Up 19.852088 0.000000 21.671062 0.0000000 131.212371
## Andr_Inh_Down 4.674573 85.721173 0.000000 5.3638099 0.000000
## GC_Inh_Up 643.982238 0.000000 3.577026 4.2068851 210.165381
## GC_Inh_Down 0.000000 261.728337 10.030152 0.7478817 1.909251
## LivX_Inh_Up 680.541601 0.000000 4.169265 4.2194779 241.447440
## LivX_Inh_Down 0.000000 229.219257 14.477847 0.7638911 5.864338
## AhHyd_Inh_Up 10.725756 1.481887 5.170198 6.0384071 11.349242
## AhHyd_Inh_Down 5.854020 51.576644 1.465541 2.9433413 0.000000
## Estr_Inh_Down Andr_Inh_Up Andr_Inh_Down GC_Inh_Up GC_Inh_Down
## Thyr_Inh_Up 0.000000 19.85209 4.674573 643.982238 0.0000000
## Thyr_Inh_Down 113.747546 0.00000 85.721173 0.000000 261.7283374
## Ret_Inh_Up 0.000000 21.67106 0.000000 3.577026 10.0301520
## Ret_Inh_Down 4.698151 0.00000 5.363810 4.206885 0.7478817
## Estr_Inh_Up 0.000000 131.21237 0.000000 210.165381 1.9092510
## Estr_Inh_Down Inf 0.00000 195.929068 0.000000 125.6235132
## Andr_Inh_Up 0.000000 Inf 0.000000 37.842924 0.0000000
## Andr_Inh_Down 195.929068 0.00000 Inf 0.000000 60.4186984
## GC_Inh_Up 0.000000 37.84292 0.000000 Inf 0.0000000
## GC_Inh_Down 125.623513 0.00000 60.418698 0.000000 Inf
## LivX_Inh_Up 0.000000 36.27646 0.000000 462.155024 0.0000000
## LivX_Inh_Down 69.118348 0.00000 59.590522 0.000000 328.9124164
## AhHyd_Inh_Up 3.511547 169.02939 0.000000 16.074371 1.7453123
## AhHyd_Inh_Down 52.500274 0.00000 353.654463 3.940650 43.4566049
## LivX_Inh_Up LivX_Inh_Down AhHyd_Inh_Up AhHyd_Inh_Down
## Thyr_Inh_Up 680.541601 0.0000000 10.725756 5.854020
## Thyr_Inh_Down 0.000000 229.2192571 1.481887 51.576644
## Ret_Inh_Up 4.169265 14.4778467 5.170198 1.465541
## Ret_Inh_Down 4.219478 0.7638911 6.038407 2.943341
## Estr_Inh_Up 241.447440 5.8643380 11.349242 0.000000
## Estr_Inh_Down 0.000000 69.1183483 3.511547 52.500274
## Andr_Inh_Up 36.276463 0.0000000 169.029389 0.000000
## Andr_Inh_Down 0.000000 59.5905220 0.000000 353.654463
## GC_Inh_Up 462.155024 0.0000000 16.074371 3.940650
## GC_Inh_Down 0.000000 328.9124164 1.745312 43.456605
## LivX_Inh_Up Inf 0.0000000 9.075724 5.444470
## LivX_Inh_Down 0.000000 Inf 2.942282 35.230183
## AhHyd_Inh_Up 9.075724 2.9422822 Inf 0.000000
## AhHyd_Inh_Down 5.444470 35.2301826 0.000000 Inf
<- data.frame(getMatrix(OvObj, name='odds.ratio'))
OR $DEGs <- row.names(OR)
OR<- gather(OR, 'KBase', 'OR', -DEGs)
OR <- data.frame(getMatrix(OvObj, name='pval'))
PVAL $DEGs <- row.names(PVAL)
PVAL<- gather(PVAL, 'KBase', 'PVal', -DEGs)
PVAL <- data.frame(getMatrix(OvObj, name='intersection'))
NUM $DEGs <- row.names(NUM)
NUM<- gather(NUM, 'KBase', 'Numbers', -DEGs)
NUM if(! identical(OR$DEGs, PVAL$DEGs)){
stop('Inconsistecy')
}if(! identical(OR$DEGs, NUM$DEGs)){
stop('Inconsistecy')
}if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}<- mutate(OR, Pval=PVAL$PVal) %>% mutate(Numbers=NUM$Numbers)
Res
Res## DEGs KBase OR Pval Numbers
## 1 Thyr_Inh_Up Thyr_Inh_Up Inf 0.000000e+00 160
## 2 Thyr_Inh_Down Thyr_Inh_Up 0.0000000 1.000000e+00 0
## 3 Ret_Inh_Up Thyr_Inh_Up 5.3018121 2.460360e-04 8
## 4 Ret_Inh_Down Thyr_Inh_Up 2.9342197 9.792842e-05 19
## 5 Estr_Inh_Up Thyr_Inh_Up 185.2165967 8.053782e-28 17
## 6 Estr_Inh_Down Thyr_Inh_Up 0.0000000 1.000000e+00 0
## 7 Andr_Inh_Up Thyr_Inh_Up 19.8520878 6.399483e-03 2
## 8 Andr_Inh_Down Thyr_Inh_Up 4.6745733 2.015707e-01 1
## 9 GC_Inh_Up Thyr_Inh_Up 643.9822382 6.600656e-185 103
## 10 GC_Inh_Down Thyr_Inh_Up 0.0000000 1.000000e+00 0
## 11 LivX_Inh_Up Thyr_Inh_Up 680.5416006 7.156443e-193 107
## 12 LivX_Inh_Down Thyr_Inh_Up 0.0000000 1.000000e+00 0
## 13 AhHyd_Inh_Up Thyr_Inh_Up 10.7257561 9.863282e-15 22
## 14 AhHyd_Inh_Down Thyr_Inh_Up 5.8540200 1.300390e-04 8
## 15 Thyr_Inh_Up Thyr_Inh_Down 0.0000000 1.000000e+00 0
## 16 Thyr_Inh_Down Thyr_Inh_Down Inf 0.000000e+00 257
## 17 Ret_Inh_Up Thyr_Inh_Down 6.0258146 4.071963e-07 14
## 18 Ret_Inh_Down Thyr_Inh_Down 1.0466803 4.818121e-01 12
## 19 Estr_Inh_Up Thyr_Inh_Down 0.0000000 1.000000e+00 0
## 20 Estr_Inh_Down Thyr_Inh_Down 113.7475464 6.684890e-50 36
## 21 Andr_Inh_Up Thyr_Inh_Down 0.0000000 1.000000e+00 0
## 22 Andr_Inh_Down Thyr_Inh_Down 85.7211729 9.704536e-17 12
## 23 GC_Inh_Up Thyr_Inh_Down 0.0000000 1.000000e+00 0
## 24 GC_Inh_Down Thyr_Inh_Down 261.7283374 4.525907e-261 177
## 25 LivX_Inh_Up Thyr_Inh_Down 0.0000000 1.000000e+00 0
## 26 LivX_Inh_Down Thyr_Inh_Down 229.2192571 7.883616e-201 135
## 27 AhHyd_Inh_Up Thyr_Inh_Down 1.4818869 2.304721e-01 6
## 28 AhHyd_Inh_Down Thyr_Inh_Down 51.5766435 4.969385e-65 57
## 29 Thyr_Inh_Up Ret_Inh_Up 5.3018121 2.460360e-04 8
## 30 Thyr_Inh_Down Ret_Inh_Up 6.0258146 4.071963e-07 14
## 31 Ret_Inh_Up Ret_Inh_Up Inf 0.000000e+00 147
## 32 Ret_Inh_Down Ret_Inh_Up 0.0000000 1.000000e+00 0
## 33 Estr_Inh_Up Ret_Inh_Up 23.6573026 5.916284e-06 5
## 34 Estr_Inh_Down Ret_Inh_Up 0.0000000 1.000000e+00 0
## 35 Andr_Inh_Up Ret_Inh_Up 21.6710621 5.428334e-03 2
## 36 Andr_Inh_Down Ret_Inh_Up 0.0000000 1.000000e+00 0
## 37 GC_Inh_Up Ret_Inh_Up 3.5770263 1.604266e-02 5
## 38 GC_Inh_Down Ret_Inh_Up 10.0301520 3.003206e-15 24
## 39 LivX_Inh_Up Ret_Inh_Up 4.1692655 4.384561e-03 6
## 40 LivX_Inh_Down Ret_Inh_Up 14.4778467 7.649489e-18 23
## 41 AhHyd_Inh_Up Ret_Inh_Up 5.1701980 2.439886e-05 11
## 42 AhHyd_Inh_Down Ret_Inh_Up 1.4655410 4.014797e-01 2
## 43 Thyr_Inh_Up Ret_Inh_Down 2.9342197 9.792842e-05 19
## 44 Thyr_Inh_Down Ret_Inh_Down 1.0466803 4.818121e-01 12
## 45 Ret_Inh_Up Ret_Inh_Down 0.0000000 1.000000e+00 0
## 46 Ret_Inh_Down Ret_Inh_Down Inf 0.000000e+00 640
## 47 Estr_Inh_Up Ret_Inh_Down 3.8998341 2.711290e-02 4
## 48 Estr_Inh_Down Ret_Inh_Down 4.6981515 1.652791e-04 10
## 49 Andr_Inh_Up Ret_Inh_Down 0.0000000 1.000000e+00 0
## 50 Andr_Inh_Down Ret_Inh_Down 5.3638099 1.084916e-02 4
## 51 GC_Inh_Up Ret_Inh_Down 4.2068851 8.851576e-08 23
## 52 GC_Inh_Down Ret_Inh_Down 0.7478817 8.527122e-01 10
## 53 LivX_Inh_Up Ret_Inh_Down 4.2194779 4.516015e-08 24
## 54 LivX_Inh_Down Ret_Inh_Down 0.7638911 8.047628e-01 7
## 55 AhHyd_Inh_Up Ret_Inh_Down 6.0384071 1.193595e-19 48
## 56 AhHyd_Inh_Down Ret_Inh_Down 2.9433413 3.196646e-04 16
## 57 Thyr_Inh_Up Estr_Inh_Up 185.2165967 8.053782e-28 17
## 58 Thyr_Inh_Down Estr_Inh_Up 0.0000000 1.000000e+00 0
## 59 Ret_Inh_Up Estr_Inh_Up 23.6573026 5.916284e-06 5
## 60 Ret_Inh_Down Estr_Inh_Up 3.8998341 2.711290e-02 4
## 61 Estr_Inh_Up Estr_Inh_Up Inf 3.739447e-82 26
## 62 Estr_Inh_Down Estr_Inh_Up 0.0000000 1.000000e+00 0
## 63 Andr_Inh_Up Estr_Inh_Up 131.2123710 1.729647e-04 2
## 64 Andr_Inh_Down Estr_Inh_Up 0.0000000 1.000000e+00 0
## 65 GC_Inh_Up Estr_Inh_Up 210.1653805 1.080777e-28 17
## 66 GC_Inh_Down Estr_Inh_Up 1.9092510 4.174868e-01 1
## 67 LivX_Inh_Up Estr_Inh_Up 241.4474401 1.052311e-30 18
## 68 LivX_Inh_Down Estr_Inh_Up 5.8643380 5.165985e-02 2
## 69 AhHyd_Inh_Up Estr_Inh_Up 11.3492420 7.250604e-04 4
## 70 AhHyd_Inh_Down Estr_Inh_Up 0.0000000 1.000000e+00 0
## 71 Thyr_Inh_Up Estr_Inh_Down 0.0000000 1.000000e+00 0
## 72 Thyr_Inh_Down Estr_Inh_Down 113.7475464 6.684890e-50 36
## 73 Ret_Inh_Up Estr_Inh_Down 0.0000000 1.000000e+00 0
## 74 Ret_Inh_Down Estr_Inh_Down 4.6981515 1.652791e-04 10
## 75 Estr_Inh_Up Estr_Inh_Down 0.0000000 1.000000e+00 0
## 76 Estr_Inh_Down Estr_Inh_Down Inf 1.553685e-158 56
## 77 Andr_Inh_Up Estr_Inh_Down 0.0000000 1.000000e+00 0
## 78 Andr_Inh_Down Estr_Inh_Down 195.9290678 3.977371e-15 8
## 79 GC_Inh_Up Estr_Inh_Down 0.0000000 1.000000e+00 0
## 80 GC_Inh_Down Estr_Inh_Down 125.6235132 8.701825e-54 39
## 81 LivX_Inh_Up Estr_Inh_Down 0.0000000 1.000000e+00 0
## 82 LivX_Inh_Down Estr_Inh_Down 69.1183483 6.967515e-34 26
## 83 AhHyd_Inh_Up Estr_Inh_Down 3.5115472 6.045316e-02 3
## 84 AhHyd_Inh_Down Estr_Inh_Down 52.5002742 8.339853e-22 17
## 85 Thyr_Inh_Up Andr_Inh_Up 19.8520878 6.399483e-03 2
## 86 Thyr_Inh_Down Andr_Inh_Up 0.0000000 1.000000e+00 0
## 87 Ret_Inh_Up Andr_Inh_Up 21.6710621 5.428334e-03 2
## 88 Ret_Inh_Down Andr_Inh_Up 0.0000000 1.000000e+00 0
## 89 Estr_Inh_Up Andr_Inh_Up 131.2123710 1.729647e-04 2
## 90 Estr_Inh_Down Andr_Inh_Up 0.0000000 1.000000e+00 0
## 91 Andr_Inh_Up Andr_Inh_Up Inf 7.806555e-39 11
## 92 Andr_Inh_Down Andr_Inh_Up 0.0000000 1.000000e+00 0
## 93 GC_Inh_Up Andr_Inh_Up 37.8429238 1.521924e-04 3
## 94 GC_Inh_Down Andr_Inh_Up 0.0000000 1.000000e+00 0
## 95 LivX_Inh_Up Andr_Inh_Up 36.2764626 1.718767e-04 3
## 96 LivX_Inh_Down Andr_Inh_Up 0.0000000 1.000000e+00 0
## 97 AhHyd_Inh_Up Andr_Inh_Up 169.0293895 6.045054e-13 8
## 98 AhHyd_Inh_Down Andr_Inh_Up 0.0000000 1.000000e+00 0
## 99 Thyr_Inh_Up Andr_Inh_Down 4.6745733 2.015707e-01 1
## 100 Thyr_Inh_Down Andr_Inh_Down 85.7211729 9.704536e-17 12
## 101 Ret_Inh_Up Andr_Inh_Down 0.0000000 1.000000e+00 0
## 102 Ret_Inh_Down Andr_Inh_Down 5.3638099 1.084916e-02 4
## 103 Estr_Inh_Up Andr_Inh_Down 0.0000000 1.000000e+00 0
## 104 Estr_Inh_Down Andr_Inh_Down 195.9290678 3.977371e-15 8
## 105 Andr_Inh_Up Andr_Inh_Down 0.0000000 1.000000e+00 0
## 106 Andr_Inh_Down Andr_Inh_Down Inf 1.914866e-65 20
## 107 GC_Inh_Up Andr_Inh_Down 0.0000000 1.000000e+00 0
## 108 GC_Inh_Down Andr_Inh_Down 60.4186984 3.269870e-14 11
## 109 LivX_Inh_Up Andr_Inh_Down 0.0000000 1.000000e+00 0
## 110 LivX_Inh_Down Andr_Inh_Down 59.5905220 2.742714e-12 9
## 111 AhHyd_Inh_Up Andr_Inh_Down 0.0000000 1.000000e+00 0
## 112 AhHyd_Inh_Down Andr_Inh_Down 353.6544634 2.497908e-27 15
## 113 Thyr_Inh_Up GC_Inh_Up 643.9822382 6.600656e-185 103
## 114 Thyr_Inh_Down GC_Inh_Up 0.0000000 1.000000e+00 0
## 115 Ret_Inh_Up GC_Inh_Up 3.5770263 1.604266e-02 5
## 116 Ret_Inh_Down GC_Inh_Up 4.2068851 8.851576e-08 23
## 117 Estr_Inh_Up GC_Inh_Up 210.1653805 1.080777e-28 17
## 118 Estr_Inh_Down GC_Inh_Up 0.0000000 1.000000e+00 0
## 119 Andr_Inh_Up GC_Inh_Up 37.8429238 1.521924e-04 3
## 120 Andr_Inh_Down GC_Inh_Up 0.0000000 1.000000e+00 0
## 121 GC_Inh_Up GC_Inh_Up Inf 0.000000e+00 143
## 122 GC_Inh_Down GC_Inh_Up 0.0000000 1.000000e+00 0
## 123 LivX_Inh_Up GC_Inh_Up 462.1550242 2.256262e-162 93
## 124 LivX_Inh_Down GC_Inh_Up 0.0000000 1.000000e+00 0
## 125 AhHyd_Inh_Up GC_Inh_Up 16.0743714 1.443761e-21 27
## 126 AhHyd_Inh_Down GC_Inh_Up 3.9406500 1.110745e-02 5
## 127 Thyr_Inh_Up GC_Inh_Down 0.0000000 1.000000e+00 0
## 128 Thyr_Inh_Down GC_Inh_Down 261.7283374 4.525907e-261 177
## 129 Ret_Inh_Up GC_Inh_Down 10.0301520 3.003206e-15 24
## 130 Ret_Inh_Down GC_Inh_Down 0.7478817 8.527122e-01 10
## 131 Estr_Inh_Up GC_Inh_Down 1.9092510 4.174868e-01 1
## 132 Estr_Inh_Down GC_Inh_Down 125.6235132 8.701825e-54 39
## 133 Andr_Inh_Up GC_Inh_Down 0.0000000 1.000000e+00 0
## 134 Andr_Inh_Down GC_Inh_Down 60.4186984 3.269870e-14 11
## 135 GC_Inh_Up GC_Inh_Down 0.0000000 1.000000e+00 0
## 136 GC_Inh_Down GC_Inh_Down Inf 0.000000e+00 294
## 137 LivX_Inh_Up GC_Inh_Down 0.0000000 1.000000e+00 0
## 138 LivX_Inh_Down GC_Inh_Down 328.9124164 1.370752e-237 155
## 139 AhHyd_Inh_Up GC_Inh_Down 1.7453123 1.006674e-01 8
## 140 AhHyd_Inh_Down GC_Inh_Down 43.4566049 2.156529e-61 57
## 141 Thyr_Inh_Up LivX_Inh_Up 680.5416006 7.156443e-193 107
## 142 Thyr_Inh_Down LivX_Inh_Up 0.0000000 1.000000e+00 0
## 143 Ret_Inh_Up LivX_Inh_Up 4.1692655 4.384561e-03 6
## 144 Ret_Inh_Down LivX_Inh_Up 4.2194779 4.516015e-08 24
## 145 Estr_Inh_Up LivX_Inh_Up 241.4474401 1.052311e-30 18
## 146 Estr_Inh_Down LivX_Inh_Up 0.0000000 1.000000e+00 0
## 147 Andr_Inh_Up LivX_Inh_Up 36.2764626 1.718767e-04 3
## 148 Andr_Inh_Down LivX_Inh_Up 0.0000000 1.000000e+00 0
## 149 GC_Inh_Up LivX_Inh_Up 462.1550242 2.256262e-162 93
## 150 GC_Inh_Down LivX_Inh_Up 0.0000000 1.000000e+00 0
## 151 LivX_Inh_Up LivX_Inh_Up Inf 0.000000e+00 149
## 152 LivX_Inh_Down LivX_Inh_Up 0.0000000 1.000000e+00 0
## 153 AhHyd_Inh_Up LivX_Inh_Up 9.0757236 2.683146e-11 18
## 154 AhHyd_Inh_Down LivX_Inh_Up 5.4444701 5.032755e-04 7
## 155 Thyr_Inh_Up LivX_Inh_Down 0.0000000 1.000000e+00 0
## 156 Thyr_Inh_Down LivX_Inh_Down 229.2192571 7.883616e-201 135
## 157 Ret_Inh_Up LivX_Inh_Down 14.4778467 7.649489e-18 23
## 158 Ret_Inh_Down LivX_Inh_Down 0.7638911 8.047628e-01 7
## 159 Estr_Inh_Up LivX_Inh_Down 5.8643380 5.165985e-02 2
## 160 Estr_Inh_Down LivX_Inh_Down 69.1183483 6.967515e-34 26
## 161 Andr_Inh_Up LivX_Inh_Down 0.0000000 1.000000e+00 0
## 162 Andr_Inh_Down LivX_Inh_Down 59.5905220 2.742714e-12 9
## 163 GC_Inh_Up LivX_Inh_Down 0.0000000 1.000000e+00 0
## 164 GC_Inh_Down LivX_Inh_Down 328.9124164 1.370752e-237 155
## 165 LivX_Inh_Up LivX_Inh_Down 0.0000000 1.000000e+00 0
## 166 LivX_Inh_Down LivX_Inh_Down Inf 0.000000e+00 202
## 167 AhHyd_Inh_Up LivX_Inh_Down 2.9422822 5.291673e-03 9
## 168 AhHyd_Inh_Down LivX_Inh_Down 35.2301826 4.722935e-41 39
## 169 Thyr_Inh_Up AhHyd_Inh_Up 10.7257561 9.863282e-15 22
## 170 Thyr_Inh_Down AhHyd_Inh_Up 1.4818869 2.304721e-01 6
## 171 Ret_Inh_Up AhHyd_Inh_Up 5.1701980 2.439886e-05 11
## 172 Ret_Inh_Down AhHyd_Inh_Up 6.0384071 1.193595e-19 48
## 173 Estr_Inh_Up AhHyd_Inh_Up 11.3492420 7.250604e-04 4
## 174 Estr_Inh_Down AhHyd_Inh_Up 3.5115472 6.045316e-02 3
## 175 Andr_Inh_Up AhHyd_Inh_Up 169.0293895 6.045054e-13 8
## 176 Andr_Inh_Down AhHyd_Inh_Up 0.0000000 1.000000e+00 0
## 177 GC_Inh_Up AhHyd_Inh_Up 16.0743714 1.443761e-21 27
## 178 GC_Inh_Down AhHyd_Inh_Up 1.7453123 1.006674e-01 8
## 179 LivX_Inh_Up AhHyd_Inh_Up 9.0757236 2.683146e-11 18
## 180 LivX_Inh_Down AhHyd_Inh_Up 2.9422822 5.291673e-03 9
## 181 AhHyd_Inh_Up AhHyd_Inh_Up Inf 0.000000e+00 229
## 182 AhHyd_Inh_Down AhHyd_Inh_Up 0.0000000 1.000000e+00 0
## 183 Thyr_Inh_Up AhHyd_Inh_Down 5.8540200 1.300390e-04 8
## 184 Thyr_Inh_Down AhHyd_Inh_Down 51.5766435 4.969385e-65 57
## 185 Ret_Inh_Up AhHyd_Inh_Down 1.4655410 4.014797e-01 2
## 186 Ret_Inh_Down AhHyd_Inh_Down 2.9433413 3.196646e-04 16
## 187 Estr_Inh_Up AhHyd_Inh_Down 0.0000000 1.000000e+00 0
## 188 Estr_Inh_Down AhHyd_Inh_Down 52.5002742 8.339853e-22 17
## 189 Andr_Inh_Up AhHyd_Inh_Down 0.0000000 1.000000e+00 0
## 190 Andr_Inh_Down AhHyd_Inh_Down 353.6544634 2.497908e-27 15
## 191 GC_Inh_Up AhHyd_Inh_Down 3.9406500 1.110745e-02 5
## 192 GC_Inh_Down AhHyd_Inh_Down 43.4566049 2.156529e-61 57
## 193 LivX_Inh_Up AhHyd_Inh_Down 5.4444701 5.032755e-04 7
## 194 LivX_Inh_Down AhHyd_Inh_Down 35.2301826 4.722935e-41 39
## 195 AhHyd_Inh_Up AhHyd_Inh_Down 0.0000000 1.000000e+00 0
## 196 AhHyd_Inh_Down AhHyd_Inh_Down Inf 0.000000e+00 134
<- Res
ResMod
$DEGs == ResMod$KBase, ]$OR <- 1
ResMod[ResMod$DEGs == ResMod$KBase, ]$Pval <- 1
ResMod[ResMod
ResMod## DEGs KBase OR Pval Numbers
## 1 Thyr_Inh_Up Thyr_Inh_Up 1.0000000 1.000000e+00 160
## 2 Thyr_Inh_Down Thyr_Inh_Up 0.0000000 1.000000e+00 0
## 3 Ret_Inh_Up Thyr_Inh_Up 5.3018121 2.460360e-04 8
## 4 Ret_Inh_Down Thyr_Inh_Up 2.9342197 9.792842e-05 19
## 5 Estr_Inh_Up Thyr_Inh_Up 185.2165967 8.053782e-28 17
## 6 Estr_Inh_Down Thyr_Inh_Up 0.0000000 1.000000e+00 0
## 7 Andr_Inh_Up Thyr_Inh_Up 19.8520878 6.399483e-03 2
## 8 Andr_Inh_Down Thyr_Inh_Up 4.6745733 2.015707e-01 1
## 9 GC_Inh_Up Thyr_Inh_Up 643.9822382 6.600656e-185 103
## 10 GC_Inh_Down Thyr_Inh_Up 0.0000000 1.000000e+00 0
## 11 LivX_Inh_Up Thyr_Inh_Up 680.5416006 7.156443e-193 107
## 12 LivX_Inh_Down Thyr_Inh_Up 0.0000000 1.000000e+00 0
## 13 AhHyd_Inh_Up Thyr_Inh_Up 10.7257561 9.863282e-15 22
## 14 AhHyd_Inh_Down Thyr_Inh_Up 5.8540200 1.300390e-04 8
## 15 Thyr_Inh_Up Thyr_Inh_Down 0.0000000 1.000000e+00 0
## 16 Thyr_Inh_Down Thyr_Inh_Down 1.0000000 1.000000e+00 257
## 17 Ret_Inh_Up Thyr_Inh_Down 6.0258146 4.071963e-07 14
## 18 Ret_Inh_Down Thyr_Inh_Down 1.0466803 4.818121e-01 12
## 19 Estr_Inh_Up Thyr_Inh_Down 0.0000000 1.000000e+00 0
## 20 Estr_Inh_Down Thyr_Inh_Down 113.7475464 6.684890e-50 36
## 21 Andr_Inh_Up Thyr_Inh_Down 0.0000000 1.000000e+00 0
## 22 Andr_Inh_Down Thyr_Inh_Down 85.7211729 9.704536e-17 12
## 23 GC_Inh_Up Thyr_Inh_Down 0.0000000 1.000000e+00 0
## 24 GC_Inh_Down Thyr_Inh_Down 261.7283374 4.525907e-261 177
## 25 LivX_Inh_Up Thyr_Inh_Down 0.0000000 1.000000e+00 0
## 26 LivX_Inh_Down Thyr_Inh_Down 229.2192571 7.883616e-201 135
## 27 AhHyd_Inh_Up Thyr_Inh_Down 1.4818869 2.304721e-01 6
## 28 AhHyd_Inh_Down Thyr_Inh_Down 51.5766435 4.969385e-65 57
## 29 Thyr_Inh_Up Ret_Inh_Up 5.3018121 2.460360e-04 8
## 30 Thyr_Inh_Down Ret_Inh_Up 6.0258146 4.071963e-07 14
## 31 Ret_Inh_Up Ret_Inh_Up 1.0000000 1.000000e+00 147
## 32 Ret_Inh_Down Ret_Inh_Up 0.0000000 1.000000e+00 0
## 33 Estr_Inh_Up Ret_Inh_Up 23.6573026 5.916284e-06 5
## 34 Estr_Inh_Down Ret_Inh_Up 0.0000000 1.000000e+00 0
## 35 Andr_Inh_Up Ret_Inh_Up 21.6710621 5.428334e-03 2
## 36 Andr_Inh_Down Ret_Inh_Up 0.0000000 1.000000e+00 0
## 37 GC_Inh_Up Ret_Inh_Up 3.5770263 1.604266e-02 5
## 38 GC_Inh_Down Ret_Inh_Up 10.0301520 3.003206e-15 24
## 39 LivX_Inh_Up Ret_Inh_Up 4.1692655 4.384561e-03 6
## 40 LivX_Inh_Down Ret_Inh_Up 14.4778467 7.649489e-18 23
## 41 AhHyd_Inh_Up Ret_Inh_Up 5.1701980 2.439886e-05 11
## 42 AhHyd_Inh_Down Ret_Inh_Up 1.4655410 4.014797e-01 2
## 43 Thyr_Inh_Up Ret_Inh_Down 2.9342197 9.792842e-05 19
## 44 Thyr_Inh_Down Ret_Inh_Down 1.0466803 4.818121e-01 12
## 45 Ret_Inh_Up Ret_Inh_Down 0.0000000 1.000000e+00 0
## 46 Ret_Inh_Down Ret_Inh_Down 1.0000000 1.000000e+00 640
## 47 Estr_Inh_Up Ret_Inh_Down 3.8998341 2.711290e-02 4
## 48 Estr_Inh_Down Ret_Inh_Down 4.6981515 1.652791e-04 10
## 49 Andr_Inh_Up Ret_Inh_Down 0.0000000 1.000000e+00 0
## 50 Andr_Inh_Down Ret_Inh_Down 5.3638099 1.084916e-02 4
## 51 GC_Inh_Up Ret_Inh_Down 4.2068851 8.851576e-08 23
## 52 GC_Inh_Down Ret_Inh_Down 0.7478817 8.527122e-01 10
## 53 LivX_Inh_Up Ret_Inh_Down 4.2194779 4.516015e-08 24
## 54 LivX_Inh_Down Ret_Inh_Down 0.7638911 8.047628e-01 7
## 55 AhHyd_Inh_Up Ret_Inh_Down 6.0384071 1.193595e-19 48
## 56 AhHyd_Inh_Down Ret_Inh_Down 2.9433413 3.196646e-04 16
## 57 Thyr_Inh_Up Estr_Inh_Up 185.2165967 8.053782e-28 17
## 58 Thyr_Inh_Down Estr_Inh_Up 0.0000000 1.000000e+00 0
## 59 Ret_Inh_Up Estr_Inh_Up 23.6573026 5.916284e-06 5
## 60 Ret_Inh_Down Estr_Inh_Up 3.8998341 2.711290e-02 4
## 61 Estr_Inh_Up Estr_Inh_Up 1.0000000 1.000000e+00 26
## 62 Estr_Inh_Down Estr_Inh_Up 0.0000000 1.000000e+00 0
## 63 Andr_Inh_Up Estr_Inh_Up 131.2123710 1.729647e-04 2
## 64 Andr_Inh_Down Estr_Inh_Up 0.0000000 1.000000e+00 0
## 65 GC_Inh_Up Estr_Inh_Up 210.1653805 1.080777e-28 17
## 66 GC_Inh_Down Estr_Inh_Up 1.9092510 4.174868e-01 1
## 67 LivX_Inh_Up Estr_Inh_Up 241.4474401 1.052311e-30 18
## 68 LivX_Inh_Down Estr_Inh_Up 5.8643380 5.165985e-02 2
## 69 AhHyd_Inh_Up Estr_Inh_Up 11.3492420 7.250604e-04 4
## 70 AhHyd_Inh_Down Estr_Inh_Up 0.0000000 1.000000e+00 0
## 71 Thyr_Inh_Up Estr_Inh_Down 0.0000000 1.000000e+00 0
## 72 Thyr_Inh_Down Estr_Inh_Down 113.7475464 6.684890e-50 36
## 73 Ret_Inh_Up Estr_Inh_Down 0.0000000 1.000000e+00 0
## 74 Ret_Inh_Down Estr_Inh_Down 4.6981515 1.652791e-04 10
## 75 Estr_Inh_Up Estr_Inh_Down 0.0000000 1.000000e+00 0
## 76 Estr_Inh_Down Estr_Inh_Down 1.0000000 1.000000e+00 56
## 77 Andr_Inh_Up Estr_Inh_Down 0.0000000 1.000000e+00 0
## 78 Andr_Inh_Down Estr_Inh_Down 195.9290678 3.977371e-15 8
## 79 GC_Inh_Up Estr_Inh_Down 0.0000000 1.000000e+00 0
## 80 GC_Inh_Down Estr_Inh_Down 125.6235132 8.701825e-54 39
## 81 LivX_Inh_Up Estr_Inh_Down 0.0000000 1.000000e+00 0
## 82 LivX_Inh_Down Estr_Inh_Down 69.1183483 6.967515e-34 26
## 83 AhHyd_Inh_Up Estr_Inh_Down 3.5115472 6.045316e-02 3
## 84 AhHyd_Inh_Down Estr_Inh_Down 52.5002742 8.339853e-22 17
## 85 Thyr_Inh_Up Andr_Inh_Up 19.8520878 6.399483e-03 2
## 86 Thyr_Inh_Down Andr_Inh_Up 0.0000000 1.000000e+00 0
## 87 Ret_Inh_Up Andr_Inh_Up 21.6710621 5.428334e-03 2
## 88 Ret_Inh_Down Andr_Inh_Up 0.0000000 1.000000e+00 0
## 89 Estr_Inh_Up Andr_Inh_Up 131.2123710 1.729647e-04 2
## 90 Estr_Inh_Down Andr_Inh_Up 0.0000000 1.000000e+00 0
## 91 Andr_Inh_Up Andr_Inh_Up 1.0000000 1.000000e+00 11
## 92 Andr_Inh_Down Andr_Inh_Up 0.0000000 1.000000e+00 0
## 93 GC_Inh_Up Andr_Inh_Up 37.8429238 1.521924e-04 3
## 94 GC_Inh_Down Andr_Inh_Up 0.0000000 1.000000e+00 0
## 95 LivX_Inh_Up Andr_Inh_Up 36.2764626 1.718767e-04 3
## 96 LivX_Inh_Down Andr_Inh_Up 0.0000000 1.000000e+00 0
## 97 AhHyd_Inh_Up Andr_Inh_Up 169.0293895 6.045054e-13 8
## 98 AhHyd_Inh_Down Andr_Inh_Up 0.0000000 1.000000e+00 0
## 99 Thyr_Inh_Up Andr_Inh_Down 4.6745733 2.015707e-01 1
## 100 Thyr_Inh_Down Andr_Inh_Down 85.7211729 9.704536e-17 12
## 101 Ret_Inh_Up Andr_Inh_Down 0.0000000 1.000000e+00 0
## 102 Ret_Inh_Down Andr_Inh_Down 5.3638099 1.084916e-02 4
## 103 Estr_Inh_Up Andr_Inh_Down 0.0000000 1.000000e+00 0
## 104 Estr_Inh_Down Andr_Inh_Down 195.9290678 3.977371e-15 8
## 105 Andr_Inh_Up Andr_Inh_Down 0.0000000 1.000000e+00 0
## 106 Andr_Inh_Down Andr_Inh_Down 1.0000000 1.000000e+00 20
## 107 GC_Inh_Up Andr_Inh_Down 0.0000000 1.000000e+00 0
## 108 GC_Inh_Down Andr_Inh_Down 60.4186984 3.269870e-14 11
## 109 LivX_Inh_Up Andr_Inh_Down 0.0000000 1.000000e+00 0
## 110 LivX_Inh_Down Andr_Inh_Down 59.5905220 2.742714e-12 9
## 111 AhHyd_Inh_Up Andr_Inh_Down 0.0000000 1.000000e+00 0
## 112 AhHyd_Inh_Down Andr_Inh_Down 353.6544634 2.497908e-27 15
## 113 Thyr_Inh_Up GC_Inh_Up 643.9822382 6.600656e-185 103
## 114 Thyr_Inh_Down GC_Inh_Up 0.0000000 1.000000e+00 0
## 115 Ret_Inh_Up GC_Inh_Up 3.5770263 1.604266e-02 5
## 116 Ret_Inh_Down GC_Inh_Up 4.2068851 8.851576e-08 23
## 117 Estr_Inh_Up GC_Inh_Up 210.1653805 1.080777e-28 17
## 118 Estr_Inh_Down GC_Inh_Up 0.0000000 1.000000e+00 0
## 119 Andr_Inh_Up GC_Inh_Up 37.8429238 1.521924e-04 3
## 120 Andr_Inh_Down GC_Inh_Up 0.0000000 1.000000e+00 0
## 121 GC_Inh_Up GC_Inh_Up 1.0000000 1.000000e+00 143
## 122 GC_Inh_Down GC_Inh_Up 0.0000000 1.000000e+00 0
## 123 LivX_Inh_Up GC_Inh_Up 462.1550242 2.256262e-162 93
## 124 LivX_Inh_Down GC_Inh_Up 0.0000000 1.000000e+00 0
## 125 AhHyd_Inh_Up GC_Inh_Up 16.0743714 1.443761e-21 27
## 126 AhHyd_Inh_Down GC_Inh_Up 3.9406500 1.110745e-02 5
## 127 Thyr_Inh_Up GC_Inh_Down 0.0000000 1.000000e+00 0
## 128 Thyr_Inh_Down GC_Inh_Down 261.7283374 4.525907e-261 177
## 129 Ret_Inh_Up GC_Inh_Down 10.0301520 3.003206e-15 24
## 130 Ret_Inh_Down GC_Inh_Down 0.7478817 8.527122e-01 10
## 131 Estr_Inh_Up GC_Inh_Down 1.9092510 4.174868e-01 1
## 132 Estr_Inh_Down GC_Inh_Down 125.6235132 8.701825e-54 39
## 133 Andr_Inh_Up GC_Inh_Down 0.0000000 1.000000e+00 0
## 134 Andr_Inh_Down GC_Inh_Down 60.4186984 3.269870e-14 11
## 135 GC_Inh_Up GC_Inh_Down 0.0000000 1.000000e+00 0
## 136 GC_Inh_Down GC_Inh_Down 1.0000000 1.000000e+00 294
## 137 LivX_Inh_Up GC_Inh_Down 0.0000000 1.000000e+00 0
## 138 LivX_Inh_Down GC_Inh_Down 328.9124164 1.370752e-237 155
## 139 AhHyd_Inh_Up GC_Inh_Down 1.7453123 1.006674e-01 8
## 140 AhHyd_Inh_Down GC_Inh_Down 43.4566049 2.156529e-61 57
## 141 Thyr_Inh_Up LivX_Inh_Up 680.5416006 7.156443e-193 107
## 142 Thyr_Inh_Down LivX_Inh_Up 0.0000000 1.000000e+00 0
## 143 Ret_Inh_Up LivX_Inh_Up 4.1692655 4.384561e-03 6
## 144 Ret_Inh_Down LivX_Inh_Up 4.2194779 4.516015e-08 24
## 145 Estr_Inh_Up LivX_Inh_Up 241.4474401 1.052311e-30 18
## 146 Estr_Inh_Down LivX_Inh_Up 0.0000000 1.000000e+00 0
## 147 Andr_Inh_Up LivX_Inh_Up 36.2764626 1.718767e-04 3
## 148 Andr_Inh_Down LivX_Inh_Up 0.0000000 1.000000e+00 0
## 149 GC_Inh_Up LivX_Inh_Up 462.1550242 2.256262e-162 93
## 150 GC_Inh_Down LivX_Inh_Up 0.0000000 1.000000e+00 0
## 151 LivX_Inh_Up LivX_Inh_Up 1.0000000 1.000000e+00 149
## 152 LivX_Inh_Down LivX_Inh_Up 0.0000000 1.000000e+00 0
## 153 AhHyd_Inh_Up LivX_Inh_Up 9.0757236 2.683146e-11 18
## 154 AhHyd_Inh_Down LivX_Inh_Up 5.4444701 5.032755e-04 7
## 155 Thyr_Inh_Up LivX_Inh_Down 0.0000000 1.000000e+00 0
## 156 Thyr_Inh_Down LivX_Inh_Down 229.2192571 7.883616e-201 135
## 157 Ret_Inh_Up LivX_Inh_Down 14.4778467 7.649489e-18 23
## 158 Ret_Inh_Down LivX_Inh_Down 0.7638911 8.047628e-01 7
## 159 Estr_Inh_Up LivX_Inh_Down 5.8643380 5.165985e-02 2
## 160 Estr_Inh_Down LivX_Inh_Down 69.1183483 6.967515e-34 26
## 161 Andr_Inh_Up LivX_Inh_Down 0.0000000 1.000000e+00 0
## 162 Andr_Inh_Down LivX_Inh_Down 59.5905220 2.742714e-12 9
## 163 GC_Inh_Up LivX_Inh_Down 0.0000000 1.000000e+00 0
## 164 GC_Inh_Down LivX_Inh_Down 328.9124164 1.370752e-237 155
## 165 LivX_Inh_Up LivX_Inh_Down 0.0000000 1.000000e+00 0
## 166 LivX_Inh_Down LivX_Inh_Down 1.0000000 1.000000e+00 202
## 167 AhHyd_Inh_Up LivX_Inh_Down 2.9422822 5.291673e-03 9
## 168 AhHyd_Inh_Down LivX_Inh_Down 35.2301826 4.722935e-41 39
## 169 Thyr_Inh_Up AhHyd_Inh_Up 10.7257561 9.863282e-15 22
## 170 Thyr_Inh_Down AhHyd_Inh_Up 1.4818869 2.304721e-01 6
## 171 Ret_Inh_Up AhHyd_Inh_Up 5.1701980 2.439886e-05 11
## 172 Ret_Inh_Down AhHyd_Inh_Up 6.0384071 1.193595e-19 48
## 173 Estr_Inh_Up AhHyd_Inh_Up 11.3492420 7.250604e-04 4
## 174 Estr_Inh_Down AhHyd_Inh_Up 3.5115472 6.045316e-02 3
## 175 Andr_Inh_Up AhHyd_Inh_Up 169.0293895 6.045054e-13 8
## 176 Andr_Inh_Down AhHyd_Inh_Up 0.0000000 1.000000e+00 0
## 177 GC_Inh_Up AhHyd_Inh_Up 16.0743714 1.443761e-21 27
## 178 GC_Inh_Down AhHyd_Inh_Up 1.7453123 1.006674e-01 8
## 179 LivX_Inh_Up AhHyd_Inh_Up 9.0757236 2.683146e-11 18
## 180 LivX_Inh_Down AhHyd_Inh_Up 2.9422822 5.291673e-03 9
## 181 AhHyd_Inh_Up AhHyd_Inh_Up 1.0000000 1.000000e+00 229
## 182 AhHyd_Inh_Down AhHyd_Inh_Up 0.0000000 1.000000e+00 0
## 183 Thyr_Inh_Up AhHyd_Inh_Down 5.8540200 1.300390e-04 8
## 184 Thyr_Inh_Down AhHyd_Inh_Down 51.5766435 4.969385e-65 57
## 185 Ret_Inh_Up AhHyd_Inh_Down 1.4655410 4.014797e-01 2
## 186 Ret_Inh_Down AhHyd_Inh_Down 2.9433413 3.196646e-04 16
## 187 Estr_Inh_Up AhHyd_Inh_Down 0.0000000 1.000000e+00 0
## 188 Estr_Inh_Down AhHyd_Inh_Down 52.5002742 8.339853e-22 17
## 189 Andr_Inh_Up AhHyd_Inh_Down 0.0000000 1.000000e+00 0
## 190 Andr_Inh_Down AhHyd_Inh_Down 353.6544634 2.497908e-27 15
## 191 GC_Inh_Up AhHyd_Inh_Down 3.9406500 1.110745e-02 5
## 192 GC_Inh_Down AhHyd_Inh_Down 43.4566049 2.156529e-61 57
## 193 LivX_Inh_Up AhHyd_Inh_Down 5.4444701 5.032755e-04 7
## 194 LivX_Inh_Down AhHyd_Inh_Down 35.2301826 4.722935e-41 39
## 195 AhHyd_Inh_Up AhHyd_Inh_Down 0.0000000 1.000000e+00 0
## 196 AhHyd_Inh_Down AhHyd_Inh_Down 1.0000000 1.000000e+00 134
I select as significant overlaps having an OR > 2 and at least 25 overlapping genes. Dots are shown for PVals < 0.01 (set in the plot). Max value in the plot must be set according to minimum PVal to avoid dots not to be shown.
<- dplyr::filter(ResMod, OR > 2) %>% dplyr::filter(Numbers > 25)
ResSel min(ResSel$Pval)
## [1] 4.525907e-261
max(ResSel$OR)
## [1] 680.5416
<- ggplot(ResSel, aes(DEGs, KBase, label=Numbers)) +
Dot geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1)) +
ggtitle('Overlap across Inhibitor-modulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_Inhibitor.pdf'), width=8, height=8)
<- c('Thyr_Inh_Up', 'Thyr_Inh_Down', 'Ret_Inh_Up', 'Ret_Inh_Down', 'LivX_Inh_Up', 'LivX_Inh_Down')
Path <- ResSel[ResSel$DEGs %in% Path & ResSel$KBase %in% Path, ]
ResPath
ResPath## DEGs KBase OR Pval Numbers
## 2 LivX_Inh_Up Thyr_Inh_Up 680.5416 7.156443e-193 107
## 5 LivX_Inh_Down Thyr_Inh_Down 229.2193 7.883616e-201 135
## 18 Thyr_Inh_Up LivX_Inh_Up 680.5416 7.156443e-193 107
## 20 Thyr_Inh_Down LivX_Inh_Down 229.2193 7.883616e-201 135
<- dplyr::filter(ResPath, OR > 2) %>% dplyr::filter(Numbers > 25)
ResPath min(ResPath$Pval)
## [1] 7.883616e-201
max(ResPath$OR)
## [1] 680.5416
<- ggplot(ResPath, aes(DEGs, KBase, label=Numbers)) +
Dot geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1))+
ggtitle('Overlap across Ihibitor-modulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_Inhibitor_Selected.pdf'), width=8, height=8)
<- list(
DEGs_UpReg
Thyr_Ag= row.names(DEA$Thyr$Agonist$DEGs[DEA$Thyr$Agonist$DEGs$log2FoldChange > 0, ]),
Thyr_Inh= row.names(DEA$Thyr$Inhibitor$DEGs[DEA$Thyr$Inhibitor$DEGs$log2FoldChange > 0, ]),
Ret_Ag= row.names(DEA$Ret$Agonist$DEGs[DEA$Ret$Agonist$DEGs$log2FoldChange > 0, ]),
Ret_Inh= row.names(DEA$Ret$Inhibitor$DEGs[DEA$Ret$Inhibitor$DEGs$log2FoldChange > 0, ]),
Estr_Ag= row.names(DEA$Estr$Agonist$DEGs[DEA$Estr$Agonist$DEGs$log2FoldChange > 0, ]),
Estr_Inh= row.names(DEA$Estr$Inhibitor$DEGs[DEA$Estr$Inhibitor$DEGs$log2FoldChange > 0, ]),
Andr_Ag= row.names(DEA$Andr$Agonist$DEGs[DEA$Andr$Agonist$DEGs$log2FoldChange > 0, ]),
Andr_Inh= row.names(DEA$Andr$Inhibitor$DEGs[DEA$Andr$Inhibitor$DEGs$log2FoldChange > 0, ]),
GC_Ag= row.names(DEA$GC$Agonist$DEGs[DEA$GC$Agonist$DEGs$log2FoldChange > 0, ]),
GC_Inh= row.names(DEA$GC$Inhibitor$DEGs[DEA$GC$Inhibitor$DEGs$log2FoldChange > 0, ]),
LivX_Ag= row.names(DEA$LivX$Agonist$DEGs[DEA$LivX$Agonist$DEGs$log2FoldChange > 0, ]),
LivX_Inh= row.names(DEA$LivX$Inhibitor$DEGs[DEA$LivX$Inhibitor$DEGs$log2FoldChange > 0, ]),
AhHyd_Ag= row.names(DEA$AhHyd$Agonist$DEGs[DEA$AhHyd$Agonist$DEGs$log2FoldChange > 0, ]),
AhHyd_Inh= row.names(DEA$AhHyd$Inhibitor$DEGs[DEA$AhHyd$Inhibitor$DEGs$log2FoldChange > 0, ])
)
<- row.names(DEA$Ret$Inhibitor$Res) %>% unique()
Universe length(Universe)
## [1] 14305
<- newGOM(DEGs_UpReg, DEGs_UpReg, genome.size=length(Universe))
OvObj print(OvObj)
## A GeneOverlapMatrix object:
## ###### Intersection ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Estr_Inh Andr_Ag Andr_Inh
## Thyr_Ag 78 12 48 2 1 4 3 1
## Thyr_Inh 12 160 56 8 1 17 88 2
## Ret_Ag 48 56 1861 43 1 11 58 3
## Ret_Inh 2 8 43 147 1 5 12 2
## Estr_Ag 1 1 1 1 1 1 1 1
## Estr_Inh 4 17 11 5 1 26 10 2
## Andr_Ag 3 88 58 12 1 10 197 3
## Andr_Inh 1 2 3 2 1 2 3 11
## GC_Ag 1 1 4 3 1 2 3 1
## GC_Inh 11 103 52 5 1 17 67 3
## LivX_Ag 1 1 2 1 1 3 1 1
## LivX_Inh 15 107 68 6 1 18 77 3
## AhHyd_Ag 2 9 2 2 1 4 3 3
## AhHyd_Inh 13 22 69 11 1 4 2 8
## GC_Ag GC_Inh LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 1 11 1 15 2 13
## Thyr_Inh 1 103 1 107 9 22
## Ret_Ag 4 52 2 68 2 69
## Ret_Inh 3 5 1 6 2 11
## Estr_Ag 1 1 1 1 1 1
## Estr_Inh 2 17 3 18 4 4
## Andr_Ag 3 67 1 77 3 2
## Andr_Inh 1 3 1 3 3 8
## GC_Ag 6 1 1 1 1 1
## GC_Inh 1 143 1 93 12 27
## LivX_Ag 1 1 10 1 1 1
## LivX_Inh 1 93 1 149 9 18
## AhHyd_Ag 1 12 1 9 20 11
## AhHyd_Inh 1 27 1 18 11 229
## ###### P-value ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag
## Thyr_Ag 1.040621e-209 5.813662e-11 1.137907e-23 1.911799e-01 5.452639e-03
## Thyr_Inh 5.813662e-11 0.000000e+00 7.635477e-13 2.460360e-04 1.118490e-02
## Ret_Ag 1.137907e-23 7.635477e-13 0.000000e+00 1.482210e-07 1.300944e-01
## Ret_Inh 1.911799e-01 2.460360e-04 1.482210e-07 0.000000e+00 1.027613e-02
## Estr_Ag 5.452639e-03 1.118490e-02 1.300944e-01 1.027613e-02 6.990563e-05
## Estr_Inh 1.116213e-05 8.053782e-28 2.073836e-04 5.916284e-06 1.817546e-03
## Andr_Ag 9.265938e-02 4.507804e-128 8.016126e-10 8.798784e-07 1.377141e-02
## Andr_Inh 5.839013e-02 6.399483e-03 1.634049e-01 5.428334e-03 7.689619e-04
## GC_Ag 3.227866e-02 6.527171e-02 3.442533e-03 2.078855e-05 4.194338e-04
## GC_Inh 2.966445e-10 6.600656e-185 9.114956e-13 1.604266e-02 9.996505e-03
## LivX_Ag 5.322409e-02 1.064159e-01 3.807545e-01 9.816670e-02 6.990563e-04
## LivX_Inh 2.241978e-15 7.156443e-193 1.134878e-22 4.384561e-03 1.041594e-02
## AhHyd_Ag 5.232939e-03 3.302718e-13 7.544395e-01 1.765347e-02 1.398113e-03
## AhHyd_Inh 2.836380e-10 9.863282e-15 6.184627e-12 2.439886e-05 1.600839e-02
## Estr_Inh Andr_Ag Andr_Inh GC_Ag GC_Inh
## Thyr_Ag 1.116213e-05 9.265938e-02 5.839013e-02 3.227866e-02 2.966445e-10
## Thyr_Inh 8.053782e-28 4.507804e-128 6.399483e-03 6.527171e-02 6.600656e-185
## Ret_Ag 2.073836e-04 8.016126e-10 1.634049e-01 3.442533e-03 9.114956e-13
## Ret_Inh 5.916284e-06 8.798784e-07 5.428334e-03 2.078855e-05 1.604266e-02
## Estr_Ag 1.817546e-03 1.377141e-02 7.689619e-04 4.194338e-04 9.996505e-03
## Estr_Inh 3.739447e-82 8.559337e-13 1.729647e-04 4.743677e-05 1.080777e-28
## Andr_Ag 8.559337e-13 0.000000e+00 3.912194e-04 4.989996e-05 1.944172e-89
## Andr_Inh 1.729647e-04 3.912194e-04 7.806555e-39 4.605714e-03 1.521924e-04
## GC_Ag 4.743677e-05 4.989996e-05 4.605714e-03 8.411255e-23 5.850988e-02
## GC_Inh 1.080777e-28 1.944172e-89 1.521924e-04 5.850988e-02 0.000000e+00
## LivX_Ag 6.342562e-07 1.295240e-01 7.665468e-03 4.187745e-03 9.561473e-02
## LivX_Inh 1.052311e-30 4.583436e-108 1.718767e-04 6.090105e-02 2.256262e-162
## AhHyd_Ag 4.072111e-08 2.467071e-03 3.828855e-07 8.360865e-03 7.326313e-20
## AhHyd_Inh 7.250604e-04 8.269819e-01 6.045054e-13 9.230286e-02 1.443761e-21
## LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 5.322409e-02 2.241978e-15 5.232939e-03 2.836380e-10
## Thyr_Inh 1.064159e-01 7.156443e-193 3.302718e-13 9.863282e-15
## Ret_Ag 3.807545e-01 1.134878e-22 7.544395e-01 6.184627e-12
## Ret_Inh 9.816670e-02 4.384561e-03 1.765347e-02 2.439886e-05
## Estr_Ag 6.990563e-04 1.041594e-02 1.398113e-03 1.600839e-02
## Estr_Inh 6.342562e-07 1.052311e-30 4.072111e-08 7.250604e-04
## Andr_Ag 1.295240e-01 4.583436e-108 2.467071e-03 8.269819e-01
## Andr_Inh 7.665468e-03 1.718767e-04 3.828855e-07 6.045054e-13
## GC_Ag 4.187745e-03 6.090105e-02 8.360865e-03 9.230286e-02
## GC_Inh 9.561473e-02 2.256262e-162 7.326313e-20 1.443761e-21
## LivX_Ag 1.014497e-35 9.944025e-02 1.389784e-02 1.490741e-01
## LivX_Inh 9.944025e-02 0.000000e+00 1.723116e-13 2.683146e-11
## AhHyd_Ag 1.389784e-02 1.723116e-13 1.914866e-65 2.059397e-15
## AhHyd_Inh 1.490741e-01 2.683146e-11 2.059397e-15 0.000000e+00
## ###### Odds Ratio ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Estr_Inh
## Thyr_Ag Inf 17.280363 10.9510459 2.555403 Inf 34.834629
## Thyr_Inh 17.280363 Inf 3.6811207 5.301812 Inf 185.216597
## Ret_Ag 10.951046 3.681121 Inf 2.806160 Inf 4.926058
## Ret_Inh 2.555403 5.301812 2.8061595 Inf Inf 23.657303
## Estr_Ag Inf Inf Inf Inf Inf Inf
## Estr_Inh 34.834629 185.216597 4.9260578 23.657303 Inf Inf
## Andr_Ag 2.892986 157.363516 2.8474388 6.711052 Inf 47.041982
## Andr_Inh 18.441367 19.852088 2.5096827 21.671062 Inf 131.212371
## GC_Ag 36.835016 17.768753 13.3957228 97.967244 Inf 295.145870
## GC_Inh 17.514657 643.982238 3.9017305 3.577026 Inf 210.165381
## LivX_Ag 20.501898 9.874508 1.6723256 10.760024 Inf 263.936170
## LivX_Inh 25.007092 680.541601 5.7873430 4.169265 Inf 241.447440
## AhHyd_Ag 20.736391 76.530282 0.7427073 10.827080 Inf 161.445165
## AhHyd_Inh 12.967846 10.725756 2.9558647 5.170198 Inf 11.349242
## Andr_Ag Andr_Inh GC_Ag GC_Inh LivX_Ag LivX_Inh
## Thyr_Ag 2.8929860 18.441367 36.83502 17.514657 20.501898 25.007092
## Thyr_Inh 157.3635159 19.852088 17.76875 643.982238 9.874508 680.541601
## Ret_Ag 2.8474388 2.509683 13.39572 3.901730 1.672326 5.787343
## Ret_Inh 6.7110520 21.671062 97.96724 3.577026 10.760024 4.169265
## Estr_Ag Inf Inf Inf Inf Inf Inf
## Estr_Inh 47.0419819 131.212371 295.14587 210.165381 263.936170 241.447440
## Andr_Ag Inf 27.200310 72.58376 94.892130 7.989273 124.658220
## Andr_Inh 27.2003101 Inf 280.40936 37.842924 157.418038 36.276463
## GC_Ag 72.5837635 280.409359 Inf 19.916480 315.815143 19.102360
## GC_Inh 94.8921300 37.842924 19.91648 Inf 11.063900 462.155024
## LivX_Ag 7.9892731 157.418038 315.81514 11.063900 Inf 10.613707
## LivX_Inh 124.6582197 36.276463 19.10236 462.155024 10.613707 Inf
## AhHyd_Ag 12.8099630 309.025816 148.99012 161.275272 83.119872 82.414783
## AhHyd_Inh 0.6271927 169.029389 12.33845 16.074371 6.852651 9.075724
## AhHyd_Ag AhHyd_Inh
## Thyr_Ag 20.7363905 12.9678463
## Thyr_Inh 76.5302820 10.7257561
## Ret_Ag 0.7427073 2.9558647
## Ret_Inh 10.8270796 5.1701980
## Estr_Ag Inf Inf
## Estr_Inh 161.4451653 11.3492420
## Andr_Ag 12.8099630 0.6271927
## Andr_Inh 309.0258164 169.0293895
## GC_Ag 148.9901154 12.3384525
## GC_Inh 161.2752720 16.0743714
## LivX_Ag 83.1198722 6.8526514
## LivX_Inh 82.4147829 9.0757236
## AhHyd_Ag Inf 78.6503962
## AhHyd_Inh 78.6503962 Inf
## ###### Jaccard Index ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag
## Thyr_Ag 1.00000000 0.053097345 0.0253833950 0.008968610 0.0128205128
## Thyr_Inh 0.05309735 1.000000000 0.0284987277 0.026755853 0.0062500000
## Ret_Ag 0.02538340 0.028498728 1.0000000000 0.021882952 0.0005373455
## Ret_Inh 0.00896861 0.026755853 0.0218829517 1.000000000 0.0068027211
## Estr_Ag 0.01282051 0.006250000 0.0005373455 0.006802721 1.0000000000
## Estr_Inh 0.04000000 0.100591716 0.0058635394 0.029761905 0.0384615385
## Andr_Ag 0.01102941 0.327137546 0.0290000000 0.036144578 0.0050761421
## Andr_Inh 0.01136364 0.011834320 0.0016051364 0.012820513 0.0909090909
## GC_Ag 0.01204819 0.006060606 0.0021470746 0.020000000 0.1666666667
## GC_Inh 0.05238095 0.515000000 0.0266393443 0.017543860 0.0069930070
## LivX_Ag 0.01149425 0.005917160 0.0010700910 0.006410256 0.1000000000
## LivX_Inh 0.07075472 0.529702970 0.0350154480 0.020689655 0.0067114094
## AhHyd_Ag 0.02083333 0.052631579 0.0010643960 0.012121212 0.0500000000
## AhHyd_Inh 0.04421769 0.059945504 0.0341415141 0.030136986 0.0043668122
## Estr_Inh Andr_Ag Andr_Inh GC_Ag GC_Inh
## Thyr_Ag 0.040000000 0.011029412 0.011363636 0.012048193 0.052380952
## Thyr_Inh 0.100591716 0.327137546 0.011834320 0.006060606 0.515000000
## Ret_Ag 0.005863539 0.029000000 0.001605136 0.002147075 0.026639344
## Ret_Inh 0.029761905 0.036144578 0.012820513 0.020000000 0.017543860
## Estr_Ag 0.038461538 0.005076142 0.090909091 0.166666667 0.006993007
## Estr_Inh 1.000000000 0.046948357 0.057142857 0.066666667 0.111842105
## Andr_Ag 0.046948357 1.000000000 0.014634146 0.015000000 0.245421245
## Andr_Inh 0.057142857 0.014634146 1.000000000 0.062500000 0.019867550
## GC_Ag 0.066666667 0.015000000 0.062500000 1.000000000 0.006756757
## GC_Inh 0.111842105 0.245421245 0.019867550 0.006756757 1.000000000
## LivX_Ag 0.090909091 0.004854369 0.050000000 0.066666667 0.006578947
## LivX_Inh 0.114649682 0.286245353 0.019108280 0.006493506 0.467336683
## AhHyd_Ag 0.095238095 0.014018692 0.107142857 0.040000000 0.079470199
## AhHyd_Inh 0.015936255 0.004716981 0.034482759 0.004273504 0.078260870
## LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 0.011494253 0.070754717 0.020833333 0.044217687
## Thyr_Inh 0.005917160 0.529702970 0.052631579 0.059945504
## Ret_Ag 0.001070091 0.035015448 0.001064396 0.034141514
## Ret_Inh 0.006410256 0.020689655 0.012121212 0.030136986
## Estr_Ag 0.100000000 0.006711409 0.050000000 0.004366812
## Estr_Inh 0.090909091 0.114649682 0.095238095 0.015936255
## Andr_Ag 0.004854369 0.286245353 0.014018692 0.004716981
## Andr_Inh 0.050000000 0.019108280 0.107142857 0.034482759
## GC_Ag 0.066666667 0.006493506 0.040000000 0.004273504
## GC_Inh 0.006578947 0.467336683 0.079470199 0.078260870
## LivX_Ag 1.000000000 0.006329114 0.034482759 0.004201681
## LivX_Inh 0.006329114 1.000000000 0.056250000 0.050000000
## AhHyd_Ag 0.034482759 0.056250000 1.000000000 0.046218487
## AhHyd_Inh 0.004201681 0.050000000 0.046218487 1.000000000
getMatrix(OvObj, name='intersection')
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Estr_Inh Andr_Ag Andr_Inh
## Thyr_Ag 78 12 48 2 1 4 3 1
## Thyr_Inh 12 160 56 8 1 17 88 2
## Ret_Ag 48 56 1861 43 1 11 58 3
## Ret_Inh 2 8 43 147 1 5 12 2
## Estr_Ag 1 1 1 1 1 1 1 1
## Estr_Inh 4 17 11 5 1 26 10 2
## Andr_Ag 3 88 58 12 1 10 197 3
## Andr_Inh 1 2 3 2 1 2 3 11
## GC_Ag 1 1 4 3 1 2 3 1
## GC_Inh 11 103 52 5 1 17 67 3
## LivX_Ag 1 1 2 1 1 3 1 1
## LivX_Inh 15 107 68 6 1 18 77 3
## AhHyd_Ag 2 9 2 2 1 4 3 3
## AhHyd_Inh 13 22 69 11 1 4 2 8
## GC_Ag GC_Inh LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 1 11 1 15 2 13
## Thyr_Inh 1 103 1 107 9 22
## Ret_Ag 4 52 2 68 2 69
## Ret_Inh 3 5 1 6 2 11
## Estr_Ag 1 1 1 1 1 1
## Estr_Inh 2 17 3 18 4 4
## Andr_Ag 3 67 1 77 3 2
## Andr_Inh 1 3 1 3 3 8
## GC_Ag 6 1 1 1 1 1
## GC_Inh 1 143 1 93 12 27
## LivX_Ag 1 1 10 1 1 1
## LivX_Inh 1 93 1 149 9 18
## AhHyd_Ag 1 12 1 9 20 11
## AhHyd_Inh 1 27 1 18 11 229
getMatrix(OvObj, name='pval')
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag
## Thyr_Ag 1.040621e-209 5.813662e-11 1.137907e-23 1.911799e-01 5.452639e-03
## Thyr_Inh 5.813662e-11 0.000000e+00 7.635477e-13 2.460360e-04 1.118490e-02
## Ret_Ag 1.137907e-23 7.635477e-13 0.000000e+00 1.482210e-07 1.300944e-01
## Ret_Inh 1.911799e-01 2.460360e-04 1.482210e-07 0.000000e+00 1.027613e-02
## Estr_Ag 5.452639e-03 1.118490e-02 1.300944e-01 1.027613e-02 6.990563e-05
## Estr_Inh 1.116213e-05 8.053782e-28 2.073836e-04 5.916284e-06 1.817546e-03
## Andr_Ag 9.265938e-02 4.507804e-128 8.016126e-10 8.798784e-07 1.377141e-02
## Andr_Inh 5.839013e-02 6.399483e-03 1.634049e-01 5.428334e-03 7.689619e-04
## GC_Ag 3.227866e-02 6.527171e-02 3.442533e-03 2.078855e-05 4.194338e-04
## GC_Inh 2.966445e-10 6.600656e-185 9.114956e-13 1.604266e-02 9.996505e-03
## LivX_Ag 5.322409e-02 1.064159e-01 3.807545e-01 9.816670e-02 6.990563e-04
## LivX_Inh 2.241978e-15 7.156443e-193 1.134878e-22 4.384561e-03 1.041594e-02
## AhHyd_Ag 5.232939e-03 3.302718e-13 7.544395e-01 1.765347e-02 1.398113e-03
## AhHyd_Inh 2.836380e-10 9.863282e-15 6.184627e-12 2.439886e-05 1.600839e-02
## Estr_Inh Andr_Ag Andr_Inh GC_Ag GC_Inh
## Thyr_Ag 1.116213e-05 9.265938e-02 5.839013e-02 3.227866e-02 2.966445e-10
## Thyr_Inh 8.053782e-28 4.507804e-128 6.399483e-03 6.527171e-02 6.600656e-185
## Ret_Ag 2.073836e-04 8.016126e-10 1.634049e-01 3.442533e-03 9.114956e-13
## Ret_Inh 5.916284e-06 8.798784e-07 5.428334e-03 2.078855e-05 1.604266e-02
## Estr_Ag 1.817546e-03 1.377141e-02 7.689619e-04 4.194338e-04 9.996505e-03
## Estr_Inh 3.739447e-82 8.559337e-13 1.729647e-04 4.743677e-05 1.080777e-28
## Andr_Ag 8.559337e-13 0.000000e+00 3.912194e-04 4.989996e-05 1.944172e-89
## Andr_Inh 1.729647e-04 3.912194e-04 7.806555e-39 4.605714e-03 1.521924e-04
## GC_Ag 4.743677e-05 4.989996e-05 4.605714e-03 8.411255e-23 5.850988e-02
## GC_Inh 1.080777e-28 1.944172e-89 1.521924e-04 5.850988e-02 0.000000e+00
## LivX_Ag 6.342562e-07 1.295240e-01 7.665468e-03 4.187745e-03 9.561473e-02
## LivX_Inh 1.052311e-30 4.583436e-108 1.718767e-04 6.090105e-02 2.256262e-162
## AhHyd_Ag 4.072111e-08 2.467071e-03 3.828855e-07 8.360865e-03 7.326313e-20
## AhHyd_Inh 7.250604e-04 8.269819e-01 6.045054e-13 9.230286e-02 1.443761e-21
## LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 5.322409e-02 2.241978e-15 5.232939e-03 2.836380e-10
## Thyr_Inh 1.064159e-01 7.156443e-193 3.302718e-13 9.863282e-15
## Ret_Ag 3.807545e-01 1.134878e-22 7.544395e-01 6.184627e-12
## Ret_Inh 9.816670e-02 4.384561e-03 1.765347e-02 2.439886e-05
## Estr_Ag 6.990563e-04 1.041594e-02 1.398113e-03 1.600839e-02
## Estr_Inh 6.342562e-07 1.052311e-30 4.072111e-08 7.250604e-04
## Andr_Ag 1.295240e-01 4.583436e-108 2.467071e-03 8.269819e-01
## Andr_Inh 7.665468e-03 1.718767e-04 3.828855e-07 6.045054e-13
## GC_Ag 4.187745e-03 6.090105e-02 8.360865e-03 9.230286e-02
## GC_Inh 9.561473e-02 2.256262e-162 7.326313e-20 1.443761e-21
## LivX_Ag 1.014497e-35 9.944025e-02 1.389784e-02 1.490741e-01
## LivX_Inh 9.944025e-02 0.000000e+00 1.723116e-13 2.683146e-11
## AhHyd_Ag 1.389784e-02 1.723116e-13 1.914866e-65 2.059397e-15
## AhHyd_Inh 1.490741e-01 2.683146e-11 2.059397e-15 0.000000e+00
getMatrix(OvObj, name='odds.ratio')
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Estr_Inh
## Thyr_Ag Inf 17.280363 10.9510459 2.555403 Inf 34.834629
## Thyr_Inh 17.280363 Inf 3.6811207 5.301812 Inf 185.216597
## Ret_Ag 10.951046 3.681121 Inf 2.806160 Inf 4.926058
## Ret_Inh 2.555403 5.301812 2.8061595 Inf Inf 23.657303
## Estr_Ag Inf Inf Inf Inf Inf Inf
## Estr_Inh 34.834629 185.216597 4.9260578 23.657303 Inf Inf
## Andr_Ag 2.892986 157.363516 2.8474388 6.711052 Inf 47.041982
## Andr_Inh 18.441367 19.852088 2.5096827 21.671062 Inf 131.212371
## GC_Ag 36.835016 17.768753 13.3957228 97.967244 Inf 295.145870
## GC_Inh 17.514657 643.982238 3.9017305 3.577026 Inf 210.165381
## LivX_Ag 20.501898 9.874508 1.6723256 10.760024 Inf 263.936170
## LivX_Inh 25.007092 680.541601 5.7873430 4.169265 Inf 241.447440
## AhHyd_Ag 20.736391 76.530282 0.7427073 10.827080 Inf 161.445165
## AhHyd_Inh 12.967846 10.725756 2.9558647 5.170198 Inf 11.349242
## Andr_Ag Andr_Inh GC_Ag GC_Inh LivX_Ag LivX_Inh
## Thyr_Ag 2.8929860 18.441367 36.83502 17.514657 20.501898 25.007092
## Thyr_Inh 157.3635159 19.852088 17.76875 643.982238 9.874508 680.541601
## Ret_Ag 2.8474388 2.509683 13.39572 3.901730 1.672326 5.787343
## Ret_Inh 6.7110520 21.671062 97.96724 3.577026 10.760024 4.169265
## Estr_Ag Inf Inf Inf Inf Inf Inf
## Estr_Inh 47.0419819 131.212371 295.14587 210.165381 263.936170 241.447440
## Andr_Ag Inf 27.200310 72.58376 94.892130 7.989273 124.658220
## Andr_Inh 27.2003101 Inf 280.40936 37.842924 157.418038 36.276463
## GC_Ag 72.5837635 280.409359 Inf 19.916480 315.815143 19.102360
## GC_Inh 94.8921300 37.842924 19.91648 Inf 11.063900 462.155024
## LivX_Ag 7.9892731 157.418038 315.81514 11.063900 Inf 10.613707
## LivX_Inh 124.6582197 36.276463 19.10236 462.155024 10.613707 Inf
## AhHyd_Ag 12.8099630 309.025816 148.99012 161.275272 83.119872 82.414783
## AhHyd_Inh 0.6271927 169.029389 12.33845 16.074371 6.852651 9.075724
## AhHyd_Ag AhHyd_Inh
## Thyr_Ag 20.7363905 12.9678463
## Thyr_Inh 76.5302820 10.7257561
## Ret_Ag 0.7427073 2.9558647
## Ret_Inh 10.8270796 5.1701980
## Estr_Ag Inf Inf
## Estr_Inh 161.4451653 11.3492420
## Andr_Ag 12.8099630 0.6271927
## Andr_Inh 309.0258164 169.0293895
## GC_Ag 148.9901154 12.3384525
## GC_Inh 161.2752720 16.0743714
## LivX_Ag 83.1198722 6.8526514
## LivX_Inh 82.4147829 9.0757236
## AhHyd_Ag Inf 78.6503962
## AhHyd_Inh 78.6503962 Inf
<- data.frame(getMatrix(OvObj, name='odds.ratio'))
OR $DEGs <- row.names(OR)
OR<- gather(OR, 'KBase', 'OR', -DEGs)
OR <- data.frame(getMatrix(OvObj, name='pval'))
PVAL $DEGs <- row.names(PVAL)
PVAL<- gather(PVAL, 'KBase', 'PVal', -DEGs)
PVAL <- data.frame(getMatrix(OvObj, name='intersection'))
NUM $DEGs <- row.names(NUM)
NUM<- gather(NUM, 'KBase', 'Numbers', -DEGs)
NUM if(! identical(OR$DEGs, PVAL$DEGs)){
stop('Inconsistecy')
}if(! identical(OR$DEGs, NUM$DEGs)){
stop('Inconsistecy')
}if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}<- mutate(OR, Pval=PVAL$PVal) %>% mutate(Numbers=NUM$Numbers)
Res
Res## DEGs KBase OR Pval Numbers
## 1 Thyr_Ag Thyr_Ag Inf 1.040621e-209 78
## 2 Thyr_Inh Thyr_Ag 17.2803631 5.813662e-11 12
## 3 Ret_Ag Thyr_Ag 10.9510459 1.137907e-23 48
## 4 Ret_Inh Thyr_Ag 2.5554025 1.911799e-01 2
## 5 Estr_Ag Thyr_Ag Inf 5.452639e-03 1
## 6 Estr_Inh Thyr_Ag 34.8346290 1.116213e-05 4
## 7 Andr_Ag Thyr_Ag 2.8929860 9.265938e-02 3
## 8 Andr_Inh Thyr_Ag 18.4413674 5.839013e-02 1
## 9 GC_Ag Thyr_Ag 36.8350164 3.227866e-02 1
## 10 GC_Inh Thyr_Ag 17.5146569 2.966445e-10 11
## 11 LivX_Ag Thyr_Ag 20.5018984 5.322409e-02 1
## 12 LivX_Inh Thyr_Ag 25.0070923 2.241978e-15 15
## 13 AhHyd_Ag Thyr_Ag 20.7363905 5.232939e-03 2
## 14 AhHyd_Inh Thyr_Ag 12.9678463 2.836380e-10 13
## 15 Thyr_Ag Thyr_Inh 17.2803631 5.813662e-11 12
## 16 Thyr_Inh Thyr_Inh Inf 0.000000e+00 160
## 17 Ret_Ag Thyr_Inh 3.6811207 7.635477e-13 56
## 18 Ret_Inh Thyr_Inh 5.3018121 2.460360e-04 8
## 19 Estr_Ag Thyr_Inh Inf 1.118490e-02 1
## 20 Estr_Inh Thyr_Inh 185.2165967 8.053782e-28 17
## 21 Andr_Ag Thyr_Inh 157.3635159 4.507804e-128 88
## 22 Andr_Inh Thyr_Inh 19.8520878 6.399483e-03 2
## 23 GC_Ag Thyr_Inh 17.7687534 6.527171e-02 1
## 24 GC_Inh Thyr_Inh 643.9822382 6.600656e-185 103
## 25 LivX_Ag Thyr_Inh 9.8745085 1.064159e-01 1
## 26 LivX_Inh Thyr_Inh 680.5416006 7.156443e-193 107
## 27 AhHyd_Ag Thyr_Inh 76.5302820 3.302718e-13 9
## 28 AhHyd_Inh Thyr_Inh 10.7257561 9.863282e-15 22
## 29 Thyr_Ag Ret_Ag 10.9510459 1.137907e-23 48
## 30 Thyr_Inh Ret_Ag 3.6811207 7.635477e-13 56
## 31 Ret_Ag Ret_Ag Inf 0.000000e+00 1861
## 32 Ret_Inh Ret_Ag 2.8061595 1.482210e-07 43
## 33 Estr_Ag Ret_Ag Inf 1.300944e-01 1
## 34 Estr_Inh Ret_Ag 4.9260578 2.073836e-04 11
## 35 Andr_Ag Ret_Ag 2.8474388 8.016126e-10 58
## 36 Andr_Inh Ret_Ag 2.5096827 1.634049e-01 3
## 37 GC_Ag Ret_Ag 13.3957228 3.442533e-03 4
## 38 GC_Inh Ret_Ag 3.9017305 9.114956e-13 52
## 39 LivX_Ag Ret_Ag 1.6723256 3.807545e-01 2
## 40 LivX_Inh Ret_Ag 5.7873430 1.134878e-22 68
## 41 AhHyd_Ag Ret_Ag 0.7427073 7.544395e-01 2
## 42 AhHyd_Inh Ret_Ag 2.9558647 6.184627e-12 69
## 43 Thyr_Ag Ret_Inh 2.5554025 1.911799e-01 2
## 44 Thyr_Inh Ret_Inh 5.3018121 2.460360e-04 8
## 45 Ret_Ag Ret_Inh 2.8061595 1.482210e-07 43
## 46 Ret_Inh Ret_Inh Inf 0.000000e+00 147
## 47 Estr_Ag Ret_Inh Inf 1.027613e-02 1
## 48 Estr_Inh Ret_Inh 23.6573026 5.916284e-06 5
## 49 Andr_Ag Ret_Inh 6.7110520 8.798784e-07 12
## 50 Andr_Inh Ret_Inh 21.6710621 5.428334e-03 2
## 51 GC_Ag Ret_Inh 97.9672443 2.078855e-05 3
## 52 GC_Inh Ret_Inh 3.5770263 1.604266e-02 5
## 53 LivX_Ag Ret_Inh 10.7600236 9.816670e-02 1
## 54 LivX_Inh Ret_Inh 4.1692655 4.384561e-03 6
## 55 AhHyd_Ag Ret_Inh 10.8270796 1.765347e-02 2
## 56 AhHyd_Inh Ret_Inh 5.1701980 2.439886e-05 11
## 57 Thyr_Ag Estr_Ag Inf 5.452639e-03 1
## 58 Thyr_Inh Estr_Ag Inf 1.118490e-02 1
## 59 Ret_Ag Estr_Ag Inf 1.300944e-01 1
## 60 Ret_Inh Estr_Ag Inf 1.027613e-02 1
## 61 Estr_Ag Estr_Ag Inf 6.990563e-05 1
## 62 Estr_Inh Estr_Ag Inf 1.817546e-03 1
## 63 Andr_Ag Estr_Ag Inf 1.377141e-02 1
## 64 Andr_Inh Estr_Ag Inf 7.689619e-04 1
## 65 GC_Ag Estr_Ag Inf 4.194338e-04 1
## 66 GC_Inh Estr_Ag Inf 9.996505e-03 1
## 67 LivX_Ag Estr_Ag Inf 6.990563e-04 1
## 68 LivX_Inh Estr_Ag Inf 1.041594e-02 1
## 69 AhHyd_Ag Estr_Ag Inf 1.398113e-03 1
## 70 AhHyd_Inh Estr_Ag Inf 1.600839e-02 1
## 71 Thyr_Ag Estr_Inh 34.8346290 1.116213e-05 4
## 72 Thyr_Inh Estr_Inh 185.2165967 8.053782e-28 17
## 73 Ret_Ag Estr_Inh 4.9260578 2.073836e-04 11
## 74 Ret_Inh Estr_Inh 23.6573026 5.916284e-06 5
## 75 Estr_Ag Estr_Inh Inf 1.817546e-03 1
## 76 Estr_Inh Estr_Inh Inf 3.739447e-82 26
## 77 Andr_Ag Estr_Inh 47.0419819 8.559337e-13 10
## 78 Andr_Inh Estr_Inh 131.2123710 1.729647e-04 2
## 79 GC_Ag Estr_Inh 295.1458698 4.743677e-05 2
## 80 GC_Inh Estr_Inh 210.1653805 1.080777e-28 17
## 81 LivX_Ag Estr_Inh 263.9361702 6.342562e-07 3
## 82 LivX_Inh Estr_Inh 241.4474401 1.052311e-30 18
## 83 AhHyd_Ag Estr_Inh 161.4451653 4.072111e-08 4
## 84 AhHyd_Inh Estr_Inh 11.3492420 7.250604e-04 4
## 85 Thyr_Ag Andr_Ag 2.8929860 9.265938e-02 3
## 86 Thyr_Inh Andr_Ag 157.3635159 4.507804e-128 88
## 87 Ret_Ag Andr_Ag 2.8474388 8.016126e-10 58
## 88 Ret_Inh Andr_Ag 6.7110520 8.798784e-07 12
## 89 Estr_Ag Andr_Ag Inf 1.377141e-02 1
## 90 Estr_Inh Andr_Ag 47.0419819 8.559337e-13 10
## 91 Andr_Ag Andr_Ag Inf 0.000000e+00 197
## 92 Andr_Inh Andr_Ag 27.2003101 3.912194e-04 3
## 93 GC_Ag Andr_Ag 72.5837635 4.989996e-05 3
## 94 GC_Inh Andr_Ag 94.8921300 1.944172e-89 67
## 95 LivX_Ag Andr_Ag 7.9892731 1.295240e-01 1
## 96 LivX_Inh Andr_Ag 124.6582197 4.583436e-108 77
## 97 AhHyd_Ag Andr_Ag 12.8099630 2.467071e-03 3
## 98 AhHyd_Inh Andr_Ag 0.6271927 8.269819e-01 2
## 99 Thyr_Ag Andr_Inh 18.4413674 5.839013e-02 1
## 100 Thyr_Inh Andr_Inh 19.8520878 6.399483e-03 2
## 101 Ret_Ag Andr_Inh 2.5096827 1.634049e-01 3
## 102 Ret_Inh Andr_Inh 21.6710621 5.428334e-03 2
## 103 Estr_Ag Andr_Inh Inf 7.689619e-04 1
## 104 Estr_Inh Andr_Inh 131.2123710 1.729647e-04 2
## 105 Andr_Ag Andr_Inh 27.2003101 3.912194e-04 3
## 106 Andr_Inh Andr_Inh Inf 7.806555e-39 11
## 107 GC_Ag Andr_Inh 280.4093590 4.605714e-03 1
## 108 GC_Inh Andr_Inh 37.8429238 1.521924e-04 3
## 109 LivX_Ag Andr_Inh 157.4180384 7.665468e-03 1
## 110 LivX_Inh Andr_Inh 36.2764626 1.718767e-04 3
## 111 AhHyd_Ag Andr_Inh 309.0258164 3.828855e-07 3
## 112 AhHyd_Inh Andr_Inh 169.0293895 6.045054e-13 8
## 113 Thyr_Ag GC_Ag 36.8350164 3.227866e-02 1
## 114 Thyr_Inh GC_Ag 17.7687534 6.527171e-02 1
## 115 Ret_Ag GC_Ag 13.3957228 3.442533e-03 4
## 116 Ret_Inh GC_Ag 97.9672443 2.078855e-05 3
## 117 Estr_Ag GC_Ag Inf 4.194338e-04 1
## 118 Estr_Inh GC_Ag 295.1458698 4.743677e-05 2
## 119 Andr_Ag GC_Ag 72.5837635 4.989996e-05 3
## 120 Andr_Inh GC_Ag 280.4093590 4.605714e-03 1
## 121 GC_Ag GC_Ag Inf 8.411255e-23 6
## 122 GC_Inh GC_Ag 19.9164804 5.850988e-02 1
## 123 LivX_Ag GC_Ag 315.8151426 4.187745e-03 1
## 124 LivX_Inh GC_Ag 19.1023596 6.090105e-02 1
## 125 AhHyd_Ag GC_Ag 148.9901154 8.360865e-03 1
## 126 AhHyd_Inh GC_Ag 12.3384525 9.230286e-02 1
## 127 Thyr_Ag GC_Inh 17.5146569 2.966445e-10 11
## 128 Thyr_Inh GC_Inh 643.9822382 6.600656e-185 103
## 129 Ret_Ag GC_Inh 3.9017305 9.114956e-13 52
## 130 Ret_Inh GC_Inh 3.5770263 1.604266e-02 5
## 131 Estr_Ag GC_Inh Inf 9.996505e-03 1
## 132 Estr_Inh GC_Inh 210.1653805 1.080777e-28 17
## 133 Andr_Ag GC_Inh 94.8921300 1.944172e-89 67
## 134 Andr_Inh GC_Inh 37.8429238 1.521924e-04 3
## 135 GC_Ag GC_Inh 19.9164804 5.850988e-02 1
## 136 GC_Inh GC_Inh Inf 0.000000e+00 143
## 137 LivX_Ag GC_Inh 11.0639004 9.561473e-02 1
## 138 LivX_Inh GC_Inh 462.1550242 2.256262e-162 93
## 139 AhHyd_Ag GC_Inh 161.2752720 7.326313e-20 12
## 140 AhHyd_Inh GC_Inh 16.0743714 1.443761e-21 27
## 141 Thyr_Ag LivX_Ag 20.5018984 5.322409e-02 1
## 142 Thyr_Inh LivX_Ag 9.8745085 1.064159e-01 1
## 143 Ret_Ag LivX_Ag 1.6723256 3.807545e-01 2
## 144 Ret_Inh LivX_Ag 10.7600236 9.816670e-02 1
## 145 Estr_Ag LivX_Ag Inf 6.990563e-04 1
## 146 Estr_Inh LivX_Ag 263.9361702 6.342562e-07 3
## 147 Andr_Ag LivX_Ag 7.9892731 1.295240e-01 1
## 148 Andr_Inh LivX_Ag 157.4180384 7.665468e-03 1
## 149 GC_Ag LivX_Ag 315.8151426 4.187745e-03 1
## 150 GC_Inh LivX_Ag 11.0639004 9.561473e-02 1
## 151 LivX_Ag LivX_Ag Inf 1.014497e-35 10
## 152 LivX_Inh LivX_Ag 10.6137067 9.944025e-02 1
## 153 AhHyd_Ag LivX_Ag 83.1198722 1.389784e-02 1
## 154 AhHyd_Inh LivX_Ag 6.8526514 1.490741e-01 1
## 155 Thyr_Ag LivX_Inh 25.0070923 2.241978e-15 15
## 156 Thyr_Inh LivX_Inh 680.5416006 7.156443e-193 107
## 157 Ret_Ag LivX_Inh 5.7873430 1.134878e-22 68
## 158 Ret_Inh LivX_Inh 4.1692655 4.384561e-03 6
## 159 Estr_Ag LivX_Inh Inf 1.041594e-02 1
## 160 Estr_Inh LivX_Inh 241.4474401 1.052311e-30 18
## 161 Andr_Ag LivX_Inh 124.6582197 4.583436e-108 77
## 162 Andr_Inh LivX_Inh 36.2764626 1.718767e-04 3
## 163 GC_Ag LivX_Inh 19.1023596 6.090105e-02 1
## 164 GC_Inh LivX_Inh 462.1550242 2.256262e-162 93
## 165 LivX_Ag LivX_Inh 10.6137067 9.944025e-02 1
## 166 LivX_Inh LivX_Inh Inf 0.000000e+00 149
## 167 AhHyd_Ag LivX_Inh 82.4147829 1.723116e-13 9
## 168 AhHyd_Inh LivX_Inh 9.0757236 2.683146e-11 18
## 169 Thyr_Ag AhHyd_Ag 20.7363905 5.232939e-03 2
## 170 Thyr_Inh AhHyd_Ag 76.5302820 3.302718e-13 9
## 171 Ret_Ag AhHyd_Ag 0.7427073 7.544395e-01 2
## 172 Ret_Inh AhHyd_Ag 10.8270796 1.765347e-02 2
## 173 Estr_Ag AhHyd_Ag Inf 1.398113e-03 1
## 174 Estr_Inh AhHyd_Ag 161.4451653 4.072111e-08 4
## 175 Andr_Ag AhHyd_Ag 12.8099630 2.467071e-03 3
## 176 Andr_Inh AhHyd_Ag 309.0258164 3.828855e-07 3
## 177 GC_Ag AhHyd_Ag 148.9901154 8.360865e-03 1
## 178 GC_Inh AhHyd_Ag 161.2752720 7.326313e-20 12
## 179 LivX_Ag AhHyd_Ag 83.1198722 1.389784e-02 1
## 180 LivX_Inh AhHyd_Ag 82.4147829 1.723116e-13 9
## 181 AhHyd_Ag AhHyd_Ag Inf 1.914866e-65 20
## 182 AhHyd_Inh AhHyd_Ag 78.6503962 2.059397e-15 11
## 183 Thyr_Ag AhHyd_Inh 12.9678463 2.836380e-10 13
## 184 Thyr_Inh AhHyd_Inh 10.7257561 9.863282e-15 22
## 185 Ret_Ag AhHyd_Inh 2.9558647 6.184627e-12 69
## 186 Ret_Inh AhHyd_Inh 5.1701980 2.439886e-05 11
## 187 Estr_Ag AhHyd_Inh Inf 1.600839e-02 1
## 188 Estr_Inh AhHyd_Inh 11.3492420 7.250604e-04 4
## 189 Andr_Ag AhHyd_Inh 0.6271927 8.269819e-01 2
## 190 Andr_Inh AhHyd_Inh 169.0293895 6.045054e-13 8
## 191 GC_Ag AhHyd_Inh 12.3384525 9.230286e-02 1
## 192 GC_Inh AhHyd_Inh 16.0743714 1.443761e-21 27
## 193 LivX_Ag AhHyd_Inh 6.8526514 1.490741e-01 1
## 194 LivX_Inh AhHyd_Inh 9.0757236 2.683146e-11 18
## 195 AhHyd_Ag AhHyd_Inh 78.6503962 2.059397e-15 11
## 196 AhHyd_Inh AhHyd_Inh Inf 0.000000e+00 229
<- Res
ResMod
$DEGs == ResMod$KBase, ]$OR <- 1
ResMod[ResMod$DEGs == ResMod$KBase, ]$Pval <- 1
ResMod[ResMod
ResMod## DEGs KBase OR Pval Numbers
## 1 Thyr_Ag Thyr_Ag 1.0000000 1.000000e+00 78
## 2 Thyr_Inh Thyr_Ag 17.2803631 5.813662e-11 12
## 3 Ret_Ag Thyr_Ag 10.9510459 1.137907e-23 48
## 4 Ret_Inh Thyr_Ag 2.5554025 1.911799e-01 2
## 5 Estr_Ag Thyr_Ag Inf 5.452639e-03 1
## 6 Estr_Inh Thyr_Ag 34.8346290 1.116213e-05 4
## 7 Andr_Ag Thyr_Ag 2.8929860 9.265938e-02 3
## 8 Andr_Inh Thyr_Ag 18.4413674 5.839013e-02 1
## 9 GC_Ag Thyr_Ag 36.8350164 3.227866e-02 1
## 10 GC_Inh Thyr_Ag 17.5146569 2.966445e-10 11
## 11 LivX_Ag Thyr_Ag 20.5018984 5.322409e-02 1
## 12 LivX_Inh Thyr_Ag 25.0070923 2.241978e-15 15
## 13 AhHyd_Ag Thyr_Ag 20.7363905 5.232939e-03 2
## 14 AhHyd_Inh Thyr_Ag 12.9678463 2.836380e-10 13
## 15 Thyr_Ag Thyr_Inh 17.2803631 5.813662e-11 12
## 16 Thyr_Inh Thyr_Inh 1.0000000 1.000000e+00 160
## 17 Ret_Ag Thyr_Inh 3.6811207 7.635477e-13 56
## 18 Ret_Inh Thyr_Inh 5.3018121 2.460360e-04 8
## 19 Estr_Ag Thyr_Inh Inf 1.118490e-02 1
## 20 Estr_Inh Thyr_Inh 185.2165967 8.053782e-28 17
## 21 Andr_Ag Thyr_Inh 157.3635159 4.507804e-128 88
## 22 Andr_Inh Thyr_Inh 19.8520878 6.399483e-03 2
## 23 GC_Ag Thyr_Inh 17.7687534 6.527171e-02 1
## 24 GC_Inh Thyr_Inh 643.9822382 6.600656e-185 103
## 25 LivX_Ag Thyr_Inh 9.8745085 1.064159e-01 1
## 26 LivX_Inh Thyr_Inh 680.5416006 7.156443e-193 107
## 27 AhHyd_Ag Thyr_Inh 76.5302820 3.302718e-13 9
## 28 AhHyd_Inh Thyr_Inh 10.7257561 9.863282e-15 22
## 29 Thyr_Ag Ret_Ag 10.9510459 1.137907e-23 48
## 30 Thyr_Inh Ret_Ag 3.6811207 7.635477e-13 56
## 31 Ret_Ag Ret_Ag 1.0000000 1.000000e+00 1861
## 32 Ret_Inh Ret_Ag 2.8061595 1.482210e-07 43
## 33 Estr_Ag Ret_Ag Inf 1.300944e-01 1
## 34 Estr_Inh Ret_Ag 4.9260578 2.073836e-04 11
## 35 Andr_Ag Ret_Ag 2.8474388 8.016126e-10 58
## 36 Andr_Inh Ret_Ag 2.5096827 1.634049e-01 3
## 37 GC_Ag Ret_Ag 13.3957228 3.442533e-03 4
## 38 GC_Inh Ret_Ag 3.9017305 9.114956e-13 52
## 39 LivX_Ag Ret_Ag 1.6723256 3.807545e-01 2
## 40 LivX_Inh Ret_Ag 5.7873430 1.134878e-22 68
## 41 AhHyd_Ag Ret_Ag 0.7427073 7.544395e-01 2
## 42 AhHyd_Inh Ret_Ag 2.9558647 6.184627e-12 69
## 43 Thyr_Ag Ret_Inh 2.5554025 1.911799e-01 2
## 44 Thyr_Inh Ret_Inh 5.3018121 2.460360e-04 8
## 45 Ret_Ag Ret_Inh 2.8061595 1.482210e-07 43
## 46 Ret_Inh Ret_Inh 1.0000000 1.000000e+00 147
## 47 Estr_Ag Ret_Inh Inf 1.027613e-02 1
## 48 Estr_Inh Ret_Inh 23.6573026 5.916284e-06 5
## 49 Andr_Ag Ret_Inh 6.7110520 8.798784e-07 12
## 50 Andr_Inh Ret_Inh 21.6710621 5.428334e-03 2
## 51 GC_Ag Ret_Inh 97.9672443 2.078855e-05 3
## 52 GC_Inh Ret_Inh 3.5770263 1.604266e-02 5
## 53 LivX_Ag Ret_Inh 10.7600236 9.816670e-02 1
## 54 LivX_Inh Ret_Inh 4.1692655 4.384561e-03 6
## 55 AhHyd_Ag Ret_Inh 10.8270796 1.765347e-02 2
## 56 AhHyd_Inh Ret_Inh 5.1701980 2.439886e-05 11
## 57 Thyr_Ag Estr_Ag Inf 5.452639e-03 1
## 58 Thyr_Inh Estr_Ag Inf 1.118490e-02 1
## 59 Ret_Ag Estr_Ag Inf 1.300944e-01 1
## 60 Ret_Inh Estr_Ag Inf 1.027613e-02 1
## 61 Estr_Ag Estr_Ag 1.0000000 1.000000e+00 1
## 62 Estr_Inh Estr_Ag Inf 1.817546e-03 1
## 63 Andr_Ag Estr_Ag Inf 1.377141e-02 1
## 64 Andr_Inh Estr_Ag Inf 7.689619e-04 1
## 65 GC_Ag Estr_Ag Inf 4.194338e-04 1
## 66 GC_Inh Estr_Ag Inf 9.996505e-03 1
## 67 LivX_Ag Estr_Ag Inf 6.990563e-04 1
## 68 LivX_Inh Estr_Ag Inf 1.041594e-02 1
## 69 AhHyd_Ag Estr_Ag Inf 1.398113e-03 1
## 70 AhHyd_Inh Estr_Ag Inf 1.600839e-02 1
## 71 Thyr_Ag Estr_Inh 34.8346290 1.116213e-05 4
## 72 Thyr_Inh Estr_Inh 185.2165967 8.053782e-28 17
## 73 Ret_Ag Estr_Inh 4.9260578 2.073836e-04 11
## 74 Ret_Inh Estr_Inh 23.6573026 5.916284e-06 5
## 75 Estr_Ag Estr_Inh Inf 1.817546e-03 1
## 76 Estr_Inh Estr_Inh 1.0000000 1.000000e+00 26
## 77 Andr_Ag Estr_Inh 47.0419819 8.559337e-13 10
## 78 Andr_Inh Estr_Inh 131.2123710 1.729647e-04 2
## 79 GC_Ag Estr_Inh 295.1458698 4.743677e-05 2
## 80 GC_Inh Estr_Inh 210.1653805 1.080777e-28 17
## 81 LivX_Ag Estr_Inh 263.9361702 6.342562e-07 3
## 82 LivX_Inh Estr_Inh 241.4474401 1.052311e-30 18
## 83 AhHyd_Ag Estr_Inh 161.4451653 4.072111e-08 4
## 84 AhHyd_Inh Estr_Inh 11.3492420 7.250604e-04 4
## 85 Thyr_Ag Andr_Ag 2.8929860 9.265938e-02 3
## 86 Thyr_Inh Andr_Ag 157.3635159 4.507804e-128 88
## 87 Ret_Ag Andr_Ag 2.8474388 8.016126e-10 58
## 88 Ret_Inh Andr_Ag 6.7110520 8.798784e-07 12
## 89 Estr_Ag Andr_Ag Inf 1.377141e-02 1
## 90 Estr_Inh Andr_Ag 47.0419819 8.559337e-13 10
## 91 Andr_Ag Andr_Ag 1.0000000 1.000000e+00 197
## 92 Andr_Inh Andr_Ag 27.2003101 3.912194e-04 3
## 93 GC_Ag Andr_Ag 72.5837635 4.989996e-05 3
## 94 GC_Inh Andr_Ag 94.8921300 1.944172e-89 67
## 95 LivX_Ag Andr_Ag 7.9892731 1.295240e-01 1
## 96 LivX_Inh Andr_Ag 124.6582197 4.583436e-108 77
## 97 AhHyd_Ag Andr_Ag 12.8099630 2.467071e-03 3
## 98 AhHyd_Inh Andr_Ag 0.6271927 8.269819e-01 2
## 99 Thyr_Ag Andr_Inh 18.4413674 5.839013e-02 1
## 100 Thyr_Inh Andr_Inh 19.8520878 6.399483e-03 2
## 101 Ret_Ag Andr_Inh 2.5096827 1.634049e-01 3
## 102 Ret_Inh Andr_Inh 21.6710621 5.428334e-03 2
## 103 Estr_Ag Andr_Inh Inf 7.689619e-04 1
## 104 Estr_Inh Andr_Inh 131.2123710 1.729647e-04 2
## 105 Andr_Ag Andr_Inh 27.2003101 3.912194e-04 3
## 106 Andr_Inh Andr_Inh 1.0000000 1.000000e+00 11
## 107 GC_Ag Andr_Inh 280.4093590 4.605714e-03 1
## 108 GC_Inh Andr_Inh 37.8429238 1.521924e-04 3
## 109 LivX_Ag Andr_Inh 157.4180384 7.665468e-03 1
## 110 LivX_Inh Andr_Inh 36.2764626 1.718767e-04 3
## 111 AhHyd_Ag Andr_Inh 309.0258164 3.828855e-07 3
## 112 AhHyd_Inh Andr_Inh 169.0293895 6.045054e-13 8
## 113 Thyr_Ag GC_Ag 36.8350164 3.227866e-02 1
## 114 Thyr_Inh GC_Ag 17.7687534 6.527171e-02 1
## 115 Ret_Ag GC_Ag 13.3957228 3.442533e-03 4
## 116 Ret_Inh GC_Ag 97.9672443 2.078855e-05 3
## 117 Estr_Ag GC_Ag Inf 4.194338e-04 1
## 118 Estr_Inh GC_Ag 295.1458698 4.743677e-05 2
## 119 Andr_Ag GC_Ag 72.5837635 4.989996e-05 3
## 120 Andr_Inh GC_Ag 280.4093590 4.605714e-03 1
## 121 GC_Ag GC_Ag 1.0000000 1.000000e+00 6
## 122 GC_Inh GC_Ag 19.9164804 5.850988e-02 1
## 123 LivX_Ag GC_Ag 315.8151426 4.187745e-03 1
## 124 LivX_Inh GC_Ag 19.1023596 6.090105e-02 1
## 125 AhHyd_Ag GC_Ag 148.9901154 8.360865e-03 1
## 126 AhHyd_Inh GC_Ag 12.3384525 9.230286e-02 1
## 127 Thyr_Ag GC_Inh 17.5146569 2.966445e-10 11
## 128 Thyr_Inh GC_Inh 643.9822382 6.600656e-185 103
## 129 Ret_Ag GC_Inh 3.9017305 9.114956e-13 52
## 130 Ret_Inh GC_Inh 3.5770263 1.604266e-02 5
## 131 Estr_Ag GC_Inh Inf 9.996505e-03 1
## 132 Estr_Inh GC_Inh 210.1653805 1.080777e-28 17
## 133 Andr_Ag GC_Inh 94.8921300 1.944172e-89 67
## 134 Andr_Inh GC_Inh 37.8429238 1.521924e-04 3
## 135 GC_Ag GC_Inh 19.9164804 5.850988e-02 1
## 136 GC_Inh GC_Inh 1.0000000 1.000000e+00 143
## 137 LivX_Ag GC_Inh 11.0639004 9.561473e-02 1
## 138 LivX_Inh GC_Inh 462.1550242 2.256262e-162 93
## 139 AhHyd_Ag GC_Inh 161.2752720 7.326313e-20 12
## 140 AhHyd_Inh GC_Inh 16.0743714 1.443761e-21 27
## 141 Thyr_Ag LivX_Ag 20.5018984 5.322409e-02 1
## 142 Thyr_Inh LivX_Ag 9.8745085 1.064159e-01 1
## 143 Ret_Ag LivX_Ag 1.6723256 3.807545e-01 2
## 144 Ret_Inh LivX_Ag 10.7600236 9.816670e-02 1
## 145 Estr_Ag LivX_Ag Inf 6.990563e-04 1
## 146 Estr_Inh LivX_Ag 263.9361702 6.342562e-07 3
## 147 Andr_Ag LivX_Ag 7.9892731 1.295240e-01 1
## 148 Andr_Inh LivX_Ag 157.4180384 7.665468e-03 1
## 149 GC_Ag LivX_Ag 315.8151426 4.187745e-03 1
## 150 GC_Inh LivX_Ag 11.0639004 9.561473e-02 1
## 151 LivX_Ag LivX_Ag 1.0000000 1.000000e+00 10
## 152 LivX_Inh LivX_Ag 10.6137067 9.944025e-02 1
## 153 AhHyd_Ag LivX_Ag 83.1198722 1.389784e-02 1
## 154 AhHyd_Inh LivX_Ag 6.8526514 1.490741e-01 1
## 155 Thyr_Ag LivX_Inh 25.0070923 2.241978e-15 15
## 156 Thyr_Inh LivX_Inh 680.5416006 7.156443e-193 107
## 157 Ret_Ag LivX_Inh 5.7873430 1.134878e-22 68
## 158 Ret_Inh LivX_Inh 4.1692655 4.384561e-03 6
## 159 Estr_Ag LivX_Inh Inf 1.041594e-02 1
## 160 Estr_Inh LivX_Inh 241.4474401 1.052311e-30 18
## 161 Andr_Ag LivX_Inh 124.6582197 4.583436e-108 77
## 162 Andr_Inh LivX_Inh 36.2764626 1.718767e-04 3
## 163 GC_Ag LivX_Inh 19.1023596 6.090105e-02 1
## 164 GC_Inh LivX_Inh 462.1550242 2.256262e-162 93
## 165 LivX_Ag LivX_Inh 10.6137067 9.944025e-02 1
## 166 LivX_Inh LivX_Inh 1.0000000 1.000000e+00 149
## 167 AhHyd_Ag LivX_Inh 82.4147829 1.723116e-13 9
## 168 AhHyd_Inh LivX_Inh 9.0757236 2.683146e-11 18
## 169 Thyr_Ag AhHyd_Ag 20.7363905 5.232939e-03 2
## 170 Thyr_Inh AhHyd_Ag 76.5302820 3.302718e-13 9
## 171 Ret_Ag AhHyd_Ag 0.7427073 7.544395e-01 2
## 172 Ret_Inh AhHyd_Ag 10.8270796 1.765347e-02 2
## 173 Estr_Ag AhHyd_Ag Inf 1.398113e-03 1
## 174 Estr_Inh AhHyd_Ag 161.4451653 4.072111e-08 4
## 175 Andr_Ag AhHyd_Ag 12.8099630 2.467071e-03 3
## 176 Andr_Inh AhHyd_Ag 309.0258164 3.828855e-07 3
## 177 GC_Ag AhHyd_Ag 148.9901154 8.360865e-03 1
## 178 GC_Inh AhHyd_Ag 161.2752720 7.326313e-20 12
## 179 LivX_Ag AhHyd_Ag 83.1198722 1.389784e-02 1
## 180 LivX_Inh AhHyd_Ag 82.4147829 1.723116e-13 9
## 181 AhHyd_Ag AhHyd_Ag 1.0000000 1.000000e+00 20
## 182 AhHyd_Inh AhHyd_Ag 78.6503962 2.059397e-15 11
## 183 Thyr_Ag AhHyd_Inh 12.9678463 2.836380e-10 13
## 184 Thyr_Inh AhHyd_Inh 10.7257561 9.863282e-15 22
## 185 Ret_Ag AhHyd_Inh 2.9558647 6.184627e-12 69
## 186 Ret_Inh AhHyd_Inh 5.1701980 2.439886e-05 11
## 187 Estr_Ag AhHyd_Inh Inf 1.600839e-02 1
## 188 Estr_Inh AhHyd_Inh 11.3492420 7.250604e-04 4
## 189 Andr_Ag AhHyd_Inh 0.6271927 8.269819e-01 2
## 190 Andr_Inh AhHyd_Inh 169.0293895 6.045054e-13 8
## 191 GC_Ag AhHyd_Inh 12.3384525 9.230286e-02 1
## 192 GC_Inh AhHyd_Inh 16.0743714 1.443761e-21 27
## 193 LivX_Ag AhHyd_Inh 6.8526514 1.490741e-01 1
## 194 LivX_Inh AhHyd_Inh 9.0757236 2.683146e-11 18
## 195 AhHyd_Ag AhHyd_Inh 78.6503962 2.059397e-15 11
## 196 AhHyd_Inh AhHyd_Inh 1.0000000 1.000000e+00 229
I select as significant overlaps having an OR > 2 and at least 25 overlapping genes. Dots are shown for PVals < 0.01 (set in the plot). Max value in the plot must be set according to minimum PVal to avoid dots not to be shown.
<- viridis::cividis(100)[1:80]
cols <- dplyr::filter(ResMod, OR > 2) %>% dplyr::filter(Numbers > 25)
ResSel min(ResSel$Pval)
## [1] 7.156443e-193
max(ResSel$OR)
## [1] 680.5416
<- ggplot(ResSel, aes(DEGs, KBase, label=Numbers)) +
Dot geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1)) +
ggtitle('Overlap across upregulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_UpReg.pdf'), width=8, height=8)
Starting from already selected results, we identify only the ones related to the pathways of interest.
<- c('Thyr_Ag', 'Thyr_Inh', 'Ret_Ag', 'Ret_Inh', 'Estr_Ag','Estr_Inh', 'LivX_Ag', 'LivX_Inh')
Path <- ResSel[ResSel$DEGs %in% Path & ResSel$KBase %in% Path, ]
ResPath
ResPath## DEGs KBase OR Pval Numbers
## 1 Ret_Ag Thyr_Ag 10.951046 1.137907e-23 48
## 2 Ret_Ag Thyr_Inh 3.681121 7.635477e-13 56
## 5 LivX_Inh Thyr_Inh 680.541601 7.156443e-193 107
## 6 Thyr_Ag Ret_Ag 10.951046 1.137907e-23 48
## 7 Thyr_Inh Ret_Ag 3.681121 7.635477e-13 56
## 8 Ret_Inh Ret_Ag 2.806160 1.482210e-07 43
## 11 LivX_Inh Ret_Ag 5.787343 1.134878e-22 68
## 13 Ret_Ag Ret_Inh 2.806160 1.482210e-07 43
## 23 Thyr_Inh LivX_Inh 680.541601 7.156443e-193 107
## 24 Ret_Ag LivX_Inh 5.787343 1.134878e-22 68
min(ResPath$Pval)
## [1] 7.156443e-193
max(ResPath$OR)
## [1] 680.5416
<- ggplot(ResPath, aes(DEGs, KBase, label=Numbers)) +
Dot geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1))+
ggtitle('Overlap across up-regulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_Upreg_Selected.pdf'), width=8, height=8)
<- list(
DEGs_DownReg
Thyr_Ag= row.names(DEA$Thyr$Agonist$DEGs[DEA$Thyr$Agonist$DEGs$log2FoldChange < 0, ]),
Thyr_Inh= row.names(DEA$Thyr$Inhibitor$DEGs[DEA$Thyr$Inhibitor$DEGs$log2FoldChange < 0, ]),
Ret_Ag= row.names(DEA$Ret$Agonist$DEGs[DEA$Ret$Agonist$DEGs$log2FoldChange < 0, ]),
Ret_Inh= row.names(DEA$Ret$Inhibitor$DEGs[DEA$Ret$Inhibitor$DEGs$log2FoldChange < 0, ]),
Estr_Ag= row.names(DEA$Estr$Agonist$DEGs[DEA$Estr$Agonist$DEGs$log2FoldChange < 0, ]),
Estr_Inh= row.names(DEA$Estr$Inhibitor$DEGs[DEA$Estr$Inhibitor$DEGs$log2FoldChange < 0, ]),
Andr_Ag= row.names(DEA$Andr$Agonist$DEGs[DEA$Andr$Agonist$DEGs$log2FoldChange < 0, ]),
Andr_Inh= row.names(DEA$Andr$Inhibitor$DEGs[DEA$Andr$Inhibitor$DEGs$log2FoldChange < 0, ]),
GC_Ag= row.names(DEA$GC$Agonist$DEGs[DEA$GC$Agonist$DEGs$log2FoldChange < 0, ]),
GC_Inh= row.names(DEA$GC$Inhibitor$DEGs[DEA$GC$Inhibitor$DEGs$log2FoldChange < 0, ]),
LivX_Ag= row.names(DEA$LivX$Agonist$DEGs[DEA$LivX$Agonist$DEGs$log2FoldChange < 0, ]),
LivX_Inh= row.names(DEA$LivX$Inhibitor$DEGs[DEA$LivX$Inhibitor$DEGs$log2FoldChange < 0, ]),
AhHyd_Ag= row.names(DEA$AhHyd$Agonist$DEGs[DEA$AhHyd$Agonist$DEGs$log2FoldChange < 0, ]),
AhHyd_Inh= row.names(DEA$AhHyd$Inhibitor$DEGs[DEA$AhHyd$Inhibitor$DEGs$log2FoldChange < 0, ])
)
<- row.names(DEA$Ret$Inhibitor$Res) %>% unique()
Universe length(Universe)
## [1] 14305
<- newGOM(DEGs_DownReg, DEGs_DownReg, genome.size=length(Universe))
OvObj print(OvObj)
## A GeneOverlapMatrix object:
## ###### Intersection ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Estr_Inh Andr_Ag Andr_Inh
## Thyr_Ag 69 30 36 7 2 20 2 2
## Thyr_Inh 30 257 83 12 0 36 19 12
## Ret_Ag 36 83 1108 191 0 25 5 6
## Ret_Inh 7 12 191 640 1 10 4 4
## Estr_Ag 2 0 0 1 3 0 0 1
## Estr_Inh 20 36 25 10 0 56 4 8
## Andr_Ag 2 19 5 4 0 4 45 0
## Andr_Inh 2 12 6 4 1 8 0 20
## GC_Ag 2 2 1 9 1 1 1 1
## GC_Inh 37 177 114 10 1 39 14 11
## LivX_Ag 1 1 0 6 1 1 0 0
## LivX_Inh 25 135 75 7 1 26 15 9
## AhHyd_Ag 5 11 12 19 0 8 2 7
## AhHyd_Inh 9 57 40 16 1 17 0 15
## GC_Ag GC_Inh LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 2 37 1 25 5 9
## Thyr_Inh 2 177 1 135 11 57
## Ret_Ag 1 114 0 75 12 40
## Ret_Inh 9 10 6 7 19 16
## Estr_Ag 1 1 1 1 0 1
## Estr_Inh 1 39 1 26 8 17
## Andr_Ag 1 14 0 15 2 0
## Andr_Inh 1 11 0 9 7 15
## GC_Ag 13 3 3 3 0 7
## GC_Inh 3 294 2 155 12 57
## LivX_Ag 3 2 6 1 0 3
## LivX_Inh 3 155 1 202 7 39
## AhHyd_Ag 0 12 0 7 56 18
## AhHyd_Inh 7 57 3 39 18 134
## ###### P-value ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag
## Thyr_Ag 3.766883e-189 1.314468e-34 2.579072e-22 3.410822e-02 6.857653e-05
## Thyr_Inh 1.314468e-34 0.000000e+00 7.151751e-31 4.818121e-01 1.000000e+00
## Ret_Ag 2.579072e-22 7.151751e-31 0.000000e+00 3.312382e-65 1.000000e+00
## Ret_Inh 3.410822e-02 4.818121e-01 3.312382e-65 0.000000e+00 1.283120e-01
## Estr_Ag 6.857653e-05 1.000000e+00 1.000000e+00 1.283120e-01 2.050117e-12
## Estr_Inh 1.546010e-33 6.684890e-50 6.992332e-14 1.652791e-04 1.000000e+00
## Andr_Ag 1.986370e-02 5.628515e-22 2.675348e-01 1.408049e-01 1.000000e+00
## Andr_Inh 4.118950e-03 9.704536e-17 3.205604e-03 1.084916e-02 4.188769e-03
## GC_Ag 1.728186e-03 2.201011e-02 6.495414e-01 4.137255e-10 2.724033e-03
## GC_Inh 9.932654e-45 4.525907e-261 1.621225e-51 8.527122e-01 6.040239e-02
## LivX_Ag 2.859911e-02 1.030846e-01 1.000000e+00 7.841517e-09 1.257861e-03
## LivX_Inh 2.962314e-29 7.883616e-201 1.471045e-32 8.047628e-01 4.177030e-02
## AhHyd_Ag 7.114372e-06 3.705275e-09 1.007141e-03 1.592664e-12 1.000000e+00
## AhHyd_Inh 1.492924e-08 4.969385e-65 3.382033e-14 3.196646e-04 2.784157e-02
## Estr_Inh Andr_Ag Andr_Inh GC_Ag GC_Inh
## Thyr_Ag 1.546010e-33 1.986370e-02 4.118950e-03 1.728186e-03 9.932654e-45
## Thyr_Inh 6.684890e-50 5.628515e-22 9.704536e-17 2.201011e-02 4.525907e-261
## Ret_Ag 6.992332e-14 2.675348e-01 3.205604e-03 6.495414e-01 1.621225e-51
## Ret_Inh 1.652791e-04 1.408049e-01 1.084916e-02 4.137255e-10 8.527122e-01
## Estr_Ag 1.000000e+00 1.000000e+00 4.188769e-03 2.724033e-03 6.040239e-02
## Estr_Inh 1.553685e-158 2.784958e-05 3.977371e-15 4.973331e-02 8.701825e-54
## Andr_Ag 2.784958e-05 1.291057e-131 1.000000e+00 4.014828e-02 1.660533e-13
## Andr_Inh 3.977371e-15 1.000000e+00 1.914866e-65 1.803127e-02 3.269870e-14
## GC_Ag 4.973331e-02 4.014828e-02 1.803127e-02 5.960832e-45 2.109142e-03
## GC_Inh 8.701825e-54 1.660533e-13 3.269870e-14 2.109142e-03 0.000000e+00
## LivX_Ag 2.326364e-02 1.000000e+00 1.000000e+00 1.170823e-08 5.978819e-03
## LivX_Inh 6.967515e-34 2.492156e-17 2.742714e-12 7.147365e-04 1.370752e-237
## AhHyd_Ag 4.027221e-11 1.337955e-02 7.119400e-13 1.000000e+00 1.131389e-09
## AhHyd_Inh 8.339853e-22 1.000000e+00 2.497908e-27 8.850269e-12 2.156529e-61
## LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 2.859911e-02 2.962314e-29 7.114372e-06 1.492924e-08
## Thyr_Inh 1.030846e-01 7.883616e-201 3.705275e-09 4.969385e-65
## Ret_Ag 1.000000e+00 1.471045e-32 1.007141e-03 3.382033e-14
## Ret_Inh 7.841517e-09 8.047628e-01 1.592664e-12 3.196646e-04
## Estr_Ag 1.257861e-03 4.177030e-02 1.000000e+00 2.784157e-02
## Estr_Inh 2.326364e-02 6.967515e-34 4.027221e-11 8.339853e-22
## Andr_Ag 1.000000e+00 2.492156e-17 1.337955e-02 1.000000e+00
## Andr_Inh 1.000000e+00 2.742714e-12 7.119400e-13 2.497908e-27
## GC_Ag 1.170823e-08 7.147365e-04 1.000000e+00 8.850269e-12
## GC_Inh 5.978819e-03 1.370752e-237 1.131389e-09 2.156529e-61
## LivX_Ag 8.411255e-23 8.180412e-02 1.000000e+00 1.574745e-05
## LivX_Inh 8.180412e-02 0.000000e+00 1.302391e-05 4.722935e-41
## AhHyd_Ag 1.000000e+00 1.302391e-05 1.553685e-158 1.493590e-23
## AhHyd_Inh 1.574745e-05 4.722935e-41 1.493590e-23 0.000000e+00
## ###### Odds Ratio ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Estr_Inh
## Thyr_Ag Inf 47.389921 13.3903265 2.4260223 419.58790 160.468876
## Thyr_Inh 47.389921 Inf 6.0580526 1.0466803 0.00000 113.747546
## Ret_Ag 13.390327 6.058053 Inf 5.9130615 0.00000 9.800973
## Ret_Inh 2.426022 1.046680 5.9130615 Inf 10.68590 4.698151
## Estr_Ag 419.587900 0.000000 0.0000000 10.6858965 Inf 0.000000
## Estr_Inh 160.468876 113.747546 9.8009726 4.6981515 0.00000 Inf
## Andr_Ag 9.846678 42.984396 1.4909839 2.0897197 0.00000 26.626652
## Andr_Inh 23.529156 85.721173 5.1257938 5.3638099 369.72647 195.929068
## GC_Ag 38.505367 10.000938 0.9925479 48.6600606 572.42312 21.536778
## GC_Inh 62.681002 261.728337 8.2914649 0.7478817 23.87832 125.623513
## LivX_Ag 41.741898 10.961044 0.0000000 Inf 1380.29024 51.615824
## LivX_Inh 45.061599 229.219257 7.4697454 0.7638911 35.02564 69.118348
## AhHyd_Ag 21.699494 13.908978 3.2725273 11.2605735 0.00000 49.166593
## AhHyd_Inh 16.917689 51.576644 5.2194405 2.9433413 53.12525 52.500274
## Andr_Ag Andr_Inh GC_Ag GC_Inh LivX_Ag LivX_Inh
## Thyr_Ag 9.846678 23.529156 38.5053671 62.6810015 41.74190 45.0615986
## Thyr_Inh 42.984396 85.721173 10.0009384 261.7283374 10.96104 229.2192571
## Ret_Ag 1.490984 5.125794 0.9925479 8.2914649 0.00000 7.4697454
## Ret_Inh 2.089720 5.363810 48.6600606 0.7478817 Inf 0.7638911
## Estr_Ag 0.000000 369.726466 572.4231226 23.8783153 1380.29024 35.0256447
## Estr_Inh 26.626652 195.929068 21.5367783 125.6235132 51.61582 69.1183483
## Andr_Ag Inf 0.000000 26.9525489 22.5242987 0.00000 37.5690728
## Andr_Inh 0.000000 Inf 62.3652674 60.4186984 0.00000 59.5905220
## GC_Ag 26.952549 62.365267 Inf 14.4293865 1338.85419 21.2101381
## GC_Inh 22.524299 60.418698 14.4293865 Inf 23.95577 328.9124164
## LivX_Ag 0.000000 0.000000 1338.8541918 23.9557729 Inf 14.0229318
## LivX_Inh 37.569073 59.590522 21.2101381 328.9124164 14.02293 Inf
## AhHyd_Ag 12.226893 155.435109 0.0000000 13.4932391 0.00000 10.2925182
## AhHyd_Inh 0.000000 353.654463 129.2016419 43.4566049 108.03365 35.2301826
## AhHyd_Ag AhHyd_Inh
## Thyr_Ag 21.699494 16.917689
## Thyr_Inh 13.908978 51.576644
## Ret_Ag 3.272527 5.219441
## Ret_Inh 11.260574 2.943341
## Estr_Ag 0.000000 53.125252
## Estr_Inh 49.166593 52.500274
## Andr_Ag 12.226893 0.000000
## Andr_Inh 155.435109 353.654463
## GC_Ag 0.000000 129.201642
## GC_Inh 13.493239 43.456605
## LivX_Ag 0.000000 108.033649
## LivX_Inh 10.292518 35.230183
## AhHyd_Ag Inf 57.657098
## AhHyd_Inh 57.657098 Inf
## ###### Jaccard Index ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag
## Thyr_Ag 1.00000000 0.101351351 0.0315512708 0.009971510 0.028571429
## Thyr_Inh 0.10135135 1.000000000 0.0647425897 0.013559322 0.000000000
## Ret_Ag 0.03155127 0.064742590 1.0000000000 0.122671805 0.000000000
## Ret_Inh 0.00997151 0.013559322 0.1226718048 1.000000000 0.001557632
## Estr_Ag 0.02857143 0.000000000 0.0000000000 0.001557632 1.000000000
## Estr_Inh 0.19047619 0.129963899 0.0219490781 0.014577259 0.000000000
## Andr_Ag 0.01785714 0.067137809 0.0043554007 0.005873715 0.000000000
## Andr_Inh 0.02298851 0.045283019 0.0053475936 0.006097561 0.045454545
## GC_Ag 0.02500000 0.007462687 0.0008928571 0.013975155 0.066666667
## GC_Inh 0.11349693 0.473262032 0.0885093168 0.010822511 0.003378378
## LivX_Ag 0.01351351 0.003816794 0.0000000000 0.009375000 0.125000000
## LivX_Inh 0.10162602 0.416666667 0.0607287449 0.008383234 0.004901961
## AhHyd_Ag 0.04166667 0.036423841 0.0104166667 0.028064993 0.000000000
## AhHyd_Inh 0.04639175 0.170658683 0.0332778702 0.021108179 0.007352941
## Estr_Inh Andr_Ag Andr_Inh GC_Ag GC_Inh
## Thyr_Ag 0.19047619 0.017857143 0.022988506 0.0250000000 0.113496933
## Thyr_Inh 0.12996390 0.067137809 0.045283019 0.0074626866 0.473262032
## Ret_Ag 0.02194908 0.004355401 0.005347594 0.0008928571 0.088509317
## Ret_Inh 0.01457726 0.005873715 0.006097561 0.0139751553 0.010822511
## Estr_Ag 0.00000000 0.000000000 0.045454545 0.0666666667 0.003378378
## Estr_Inh 1.00000000 0.041237113 0.117647059 0.0147058824 0.125401929
## Andr_Ag 0.04123711 1.000000000 0.000000000 0.0175438596 0.043076923
## Andr_Inh 0.11764706 0.000000000 1.000000000 0.0312500000 0.036303630
## GC_Ag 0.01470588 0.017543860 0.031250000 1.0000000000 0.009868421
## GC_Inh 0.12540193 0.043076923 0.036303630 0.0098684211 1.000000000
## LivX_Ag 0.01639344 0.000000000 0.000000000 0.1875000000 0.006711409
## LivX_Inh 0.11206897 0.064655172 0.042253521 0.0141509434 0.454545455
## AhHyd_Ag 0.07692308 0.020202020 0.101449275 0.0000000000 0.035502959
## AhHyd_Inh 0.09826590 0.000000000 0.107913669 0.0500000000 0.153638814
## LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 0.013513514 0.101626016 0.04166667 0.046391753
## Thyr_Inh 0.003816794 0.416666667 0.03642384 0.170658683
## Ret_Ag 0.000000000 0.060728745 0.01041667 0.033277870
## Ret_Inh 0.009375000 0.008383234 0.02806499 0.021108179
## Estr_Ag 0.125000000 0.004901961 0.00000000 0.007352941
## Estr_Inh 0.016393443 0.112068966 0.07692308 0.098265896
## Andr_Ag 0.000000000 0.064655172 0.02020202 0.000000000
## Andr_Inh 0.000000000 0.042253521 0.10144928 0.107913669
## GC_Ag 0.187500000 0.014150943 0.00000000 0.050000000
## GC_Inh 0.006711409 0.454545455 0.03550296 0.153638814
## LivX_Ag 1.000000000 0.004830918 0.00000000 0.021897810
## LivX_Inh 0.004830918 1.000000000 0.02788845 0.131313131
## AhHyd_Ag 0.000000000 0.027888446 1.00000000 0.104651163
## AhHyd_Inh 0.021897810 0.131313131 0.10465116 1.000000000
getMatrix(OvObj, name='intersection')
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Estr_Inh Andr_Ag Andr_Inh
## Thyr_Ag 69 30 36 7 2 20 2 2
## Thyr_Inh 30 257 83 12 0 36 19 12
## Ret_Ag 36 83 1108 191 0 25 5 6
## Ret_Inh 7 12 191 640 1 10 4 4
## Estr_Ag 2 0 0 1 3 0 0 1
## Estr_Inh 20 36 25 10 0 56 4 8
## Andr_Ag 2 19 5 4 0 4 45 0
## Andr_Inh 2 12 6 4 1 8 0 20
## GC_Ag 2 2 1 9 1 1 1 1
## GC_Inh 37 177 114 10 1 39 14 11
## LivX_Ag 1 1 0 6 1 1 0 0
## LivX_Inh 25 135 75 7 1 26 15 9
## AhHyd_Ag 5 11 12 19 0 8 2 7
## AhHyd_Inh 9 57 40 16 1 17 0 15
## GC_Ag GC_Inh LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 2 37 1 25 5 9
## Thyr_Inh 2 177 1 135 11 57
## Ret_Ag 1 114 0 75 12 40
## Ret_Inh 9 10 6 7 19 16
## Estr_Ag 1 1 1 1 0 1
## Estr_Inh 1 39 1 26 8 17
## Andr_Ag 1 14 0 15 2 0
## Andr_Inh 1 11 0 9 7 15
## GC_Ag 13 3 3 3 0 7
## GC_Inh 3 294 2 155 12 57
## LivX_Ag 3 2 6 1 0 3
## LivX_Inh 3 155 1 202 7 39
## AhHyd_Ag 0 12 0 7 56 18
## AhHyd_Inh 7 57 3 39 18 134
getMatrix(OvObj, name='pval')
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag
## Thyr_Ag 3.766883e-189 1.314468e-34 2.579072e-22 3.410822e-02 6.857653e-05
## Thyr_Inh 1.314468e-34 0.000000e+00 7.151751e-31 4.818121e-01 1.000000e+00
## Ret_Ag 2.579072e-22 7.151751e-31 0.000000e+00 3.312382e-65 1.000000e+00
## Ret_Inh 3.410822e-02 4.818121e-01 3.312382e-65 0.000000e+00 1.283120e-01
## Estr_Ag 6.857653e-05 1.000000e+00 1.000000e+00 1.283120e-01 2.050117e-12
## Estr_Inh 1.546010e-33 6.684890e-50 6.992332e-14 1.652791e-04 1.000000e+00
## Andr_Ag 1.986370e-02 5.628515e-22 2.675348e-01 1.408049e-01 1.000000e+00
## Andr_Inh 4.118950e-03 9.704536e-17 3.205604e-03 1.084916e-02 4.188769e-03
## GC_Ag 1.728186e-03 2.201011e-02 6.495414e-01 4.137255e-10 2.724033e-03
## GC_Inh 9.932654e-45 4.525907e-261 1.621225e-51 8.527122e-01 6.040239e-02
## LivX_Ag 2.859911e-02 1.030846e-01 1.000000e+00 7.841517e-09 1.257861e-03
## LivX_Inh 2.962314e-29 7.883616e-201 1.471045e-32 8.047628e-01 4.177030e-02
## AhHyd_Ag 7.114372e-06 3.705275e-09 1.007141e-03 1.592664e-12 1.000000e+00
## AhHyd_Inh 1.492924e-08 4.969385e-65 3.382033e-14 3.196646e-04 2.784157e-02
## Estr_Inh Andr_Ag Andr_Inh GC_Ag GC_Inh
## Thyr_Ag 1.546010e-33 1.986370e-02 4.118950e-03 1.728186e-03 9.932654e-45
## Thyr_Inh 6.684890e-50 5.628515e-22 9.704536e-17 2.201011e-02 4.525907e-261
## Ret_Ag 6.992332e-14 2.675348e-01 3.205604e-03 6.495414e-01 1.621225e-51
## Ret_Inh 1.652791e-04 1.408049e-01 1.084916e-02 4.137255e-10 8.527122e-01
## Estr_Ag 1.000000e+00 1.000000e+00 4.188769e-03 2.724033e-03 6.040239e-02
## Estr_Inh 1.553685e-158 2.784958e-05 3.977371e-15 4.973331e-02 8.701825e-54
## Andr_Ag 2.784958e-05 1.291057e-131 1.000000e+00 4.014828e-02 1.660533e-13
## Andr_Inh 3.977371e-15 1.000000e+00 1.914866e-65 1.803127e-02 3.269870e-14
## GC_Ag 4.973331e-02 4.014828e-02 1.803127e-02 5.960832e-45 2.109142e-03
## GC_Inh 8.701825e-54 1.660533e-13 3.269870e-14 2.109142e-03 0.000000e+00
## LivX_Ag 2.326364e-02 1.000000e+00 1.000000e+00 1.170823e-08 5.978819e-03
## LivX_Inh 6.967515e-34 2.492156e-17 2.742714e-12 7.147365e-04 1.370752e-237
## AhHyd_Ag 4.027221e-11 1.337955e-02 7.119400e-13 1.000000e+00 1.131389e-09
## AhHyd_Inh 8.339853e-22 1.000000e+00 2.497908e-27 8.850269e-12 2.156529e-61
## LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 2.859911e-02 2.962314e-29 7.114372e-06 1.492924e-08
## Thyr_Inh 1.030846e-01 7.883616e-201 3.705275e-09 4.969385e-65
## Ret_Ag 1.000000e+00 1.471045e-32 1.007141e-03 3.382033e-14
## Ret_Inh 7.841517e-09 8.047628e-01 1.592664e-12 3.196646e-04
## Estr_Ag 1.257861e-03 4.177030e-02 1.000000e+00 2.784157e-02
## Estr_Inh 2.326364e-02 6.967515e-34 4.027221e-11 8.339853e-22
## Andr_Ag 1.000000e+00 2.492156e-17 1.337955e-02 1.000000e+00
## Andr_Inh 1.000000e+00 2.742714e-12 7.119400e-13 2.497908e-27
## GC_Ag 1.170823e-08 7.147365e-04 1.000000e+00 8.850269e-12
## GC_Inh 5.978819e-03 1.370752e-237 1.131389e-09 2.156529e-61
## LivX_Ag 8.411255e-23 8.180412e-02 1.000000e+00 1.574745e-05
## LivX_Inh 8.180412e-02 0.000000e+00 1.302391e-05 4.722935e-41
## AhHyd_Ag 1.000000e+00 1.302391e-05 1.553685e-158 1.493590e-23
## AhHyd_Inh 1.574745e-05 4.722935e-41 1.493590e-23 0.000000e+00
getMatrix(OvObj, name='odds.ratio')
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Estr_Inh
## Thyr_Ag Inf 47.389921 13.3903265 2.4260223 419.58790 160.468876
## Thyr_Inh 47.389921 Inf 6.0580526 1.0466803 0.00000 113.747546
## Ret_Ag 13.390327 6.058053 Inf 5.9130615 0.00000 9.800973
## Ret_Inh 2.426022 1.046680 5.9130615 Inf 10.68590 4.698151
## Estr_Ag 419.587900 0.000000 0.0000000 10.6858965 Inf 0.000000
## Estr_Inh 160.468876 113.747546 9.8009726 4.6981515 0.00000 Inf
## Andr_Ag 9.846678 42.984396 1.4909839 2.0897197 0.00000 26.626652
## Andr_Inh 23.529156 85.721173 5.1257938 5.3638099 369.72647 195.929068
## GC_Ag 38.505367 10.000938 0.9925479 48.6600606 572.42312 21.536778
## GC_Inh 62.681002 261.728337 8.2914649 0.7478817 23.87832 125.623513
## LivX_Ag 41.741898 10.961044 0.0000000 Inf 1380.29024 51.615824
## LivX_Inh 45.061599 229.219257 7.4697454 0.7638911 35.02564 69.118348
## AhHyd_Ag 21.699494 13.908978 3.2725273 11.2605735 0.00000 49.166593
## AhHyd_Inh 16.917689 51.576644 5.2194405 2.9433413 53.12525 52.500274
## Andr_Ag Andr_Inh GC_Ag GC_Inh LivX_Ag LivX_Inh
## Thyr_Ag 9.846678 23.529156 38.5053671 62.6810015 41.74190 45.0615986
## Thyr_Inh 42.984396 85.721173 10.0009384 261.7283374 10.96104 229.2192571
## Ret_Ag 1.490984 5.125794 0.9925479 8.2914649 0.00000 7.4697454
## Ret_Inh 2.089720 5.363810 48.6600606 0.7478817 Inf 0.7638911
## Estr_Ag 0.000000 369.726466 572.4231226 23.8783153 1380.29024 35.0256447
## Estr_Inh 26.626652 195.929068 21.5367783 125.6235132 51.61582 69.1183483
## Andr_Ag Inf 0.000000 26.9525489 22.5242987 0.00000 37.5690728
## Andr_Inh 0.000000 Inf 62.3652674 60.4186984 0.00000 59.5905220
## GC_Ag 26.952549 62.365267 Inf 14.4293865 1338.85419 21.2101381
## GC_Inh 22.524299 60.418698 14.4293865 Inf 23.95577 328.9124164
## LivX_Ag 0.000000 0.000000 1338.8541918 23.9557729 Inf 14.0229318
## LivX_Inh 37.569073 59.590522 21.2101381 328.9124164 14.02293 Inf
## AhHyd_Ag 12.226893 155.435109 0.0000000 13.4932391 0.00000 10.2925182
## AhHyd_Inh 0.000000 353.654463 129.2016419 43.4566049 108.03365 35.2301826
## AhHyd_Ag AhHyd_Inh
## Thyr_Ag 21.699494 16.917689
## Thyr_Inh 13.908978 51.576644
## Ret_Ag 3.272527 5.219441
## Ret_Inh 11.260574 2.943341
## Estr_Ag 0.000000 53.125252
## Estr_Inh 49.166593 52.500274
## Andr_Ag 12.226893 0.000000
## Andr_Inh 155.435109 353.654463
## GC_Ag 0.000000 129.201642
## GC_Inh 13.493239 43.456605
## LivX_Ag 0.000000 108.033649
## LivX_Inh 10.292518 35.230183
## AhHyd_Ag Inf 57.657098
## AhHyd_Inh 57.657098 Inf
DotPlot: data preparation
<- data.frame(getMatrix(OvObj, name='odds.ratio'))
OR $DEGs <- row.names(OR)
OR<- gather(OR, 'KBase', 'OR', -DEGs)
OR <- data.frame(getMatrix(OvObj, name='pval'))
PVAL $DEGs <- row.names(PVAL)
PVAL<- gather(PVAL, 'KBase', 'PVal', -DEGs)
PVAL <- data.frame(getMatrix(OvObj, name='intersection'))
NUM $DEGs <- row.names(NUM)
NUM<- gather(NUM, 'KBase', 'Numbers', -DEGs)
NUM if(! identical(OR$DEGs, PVAL$DEGs)){
stop('Inconsistecy')
}if(! identical(OR$DEGs, NUM$DEGs)){
stop('Inconsistecy')
}if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}<- mutate(OR, Pval=PVAL$PVal) %>% mutate(Numbers=NUM$Numbers)
Res
Res## DEGs KBase OR Pval Numbers
## 1 Thyr_Ag Thyr_Ag Inf 3.766883e-189 69
## 2 Thyr_Inh Thyr_Ag 47.3899209 1.314468e-34 30
## 3 Ret_Ag Thyr_Ag 13.3903265 2.579072e-22 36
## 4 Ret_Inh Thyr_Ag 2.4260223 3.410822e-02 7
## 5 Estr_Ag Thyr_Ag 419.5878999 6.857653e-05 2
## 6 Estr_Inh Thyr_Ag 160.4688759 1.546010e-33 20
## 7 Andr_Ag Thyr_Ag 9.8466778 1.986370e-02 2
## 8 Andr_Inh Thyr_Ag 23.5291565 4.118950e-03 2
## 9 GC_Ag Thyr_Ag 38.5053671 1.728186e-03 2
## 10 GC_Inh Thyr_Ag 62.6810015 9.932654e-45 37
## 11 LivX_Ag Thyr_Ag 41.7418977 2.859911e-02 1
## 12 LivX_Inh Thyr_Ag 45.0615986 2.962314e-29 25
## 13 AhHyd_Ag Thyr_Ag 21.6994936 7.114372e-06 5
## 14 AhHyd_Inh Thyr_Ag 16.9176895 1.492924e-08 9
## 15 Thyr_Ag Thyr_Inh 47.3899209 1.314468e-34 30
## 16 Thyr_Inh Thyr_Inh Inf 0.000000e+00 257
## 17 Ret_Ag Thyr_Inh 6.0580526 7.151751e-31 83
## 18 Ret_Inh Thyr_Inh 1.0466803 4.818121e-01 12
## 19 Estr_Ag Thyr_Inh 0.0000000 1.000000e+00 0
## 20 Estr_Inh Thyr_Inh 113.7475464 6.684890e-50 36
## 21 Andr_Ag Thyr_Inh 42.9843963 5.628515e-22 19
## 22 Andr_Inh Thyr_Inh 85.7211729 9.704536e-17 12
## 23 GC_Ag Thyr_Inh 10.0009384 2.201011e-02 2
## 24 GC_Inh Thyr_Inh 261.7283374 4.525907e-261 177
## 25 LivX_Ag Thyr_Inh 10.9610437 1.030846e-01 1
## 26 LivX_Inh Thyr_Inh 229.2192571 7.883616e-201 135
## 27 AhHyd_Ag Thyr_Inh 13.9089778 3.705275e-09 11
## 28 AhHyd_Inh Thyr_Inh 51.5766435 4.969385e-65 57
## 29 Thyr_Ag Ret_Ag 13.3903265 2.579072e-22 36
## 30 Thyr_Inh Ret_Ag 6.0580526 7.151751e-31 83
## 31 Ret_Ag Ret_Ag Inf 0.000000e+00 1108
## 32 Ret_Inh Ret_Ag 5.9130615 3.312382e-65 191
## 33 Estr_Ag Ret_Ag 0.0000000 1.000000e+00 0
## 34 Estr_Inh Ret_Ag 9.8009726 6.992332e-14 25
## 35 Andr_Ag Ret_Ag 1.4909839 2.675348e-01 5
## 36 Andr_Inh Ret_Ag 5.1257938 3.205604e-03 6
## 37 GC_Ag Ret_Ag 0.9925479 6.495414e-01 1
## 38 GC_Inh Ret_Ag 8.2914649 1.621225e-51 114
## 39 LivX_Ag Ret_Ag 0.0000000 1.000000e+00 0
## 40 LivX_Inh Ret_Ag 7.4697454 1.471045e-32 75
## 41 AhHyd_Ag Ret_Ag 3.2725273 1.007141e-03 12
## 42 AhHyd_Inh Ret_Ag 5.2194405 3.382033e-14 40
## 43 Thyr_Ag Ret_Inh 2.4260223 3.410822e-02 7
## 44 Thyr_Inh Ret_Inh 1.0466803 4.818121e-01 12
## 45 Ret_Ag Ret_Inh 5.9130615 3.312382e-65 191
## 46 Ret_Inh Ret_Inh Inf 0.000000e+00 640
## 47 Estr_Ag Ret_Inh 10.6858965 1.283120e-01 1
## 48 Estr_Inh Ret_Inh 4.6981515 1.652791e-04 10
## 49 Andr_Ag Ret_Inh 2.0897197 1.408049e-01 4
## 50 Andr_Inh Ret_Inh 5.3638099 1.084916e-02 4
## 51 GC_Ag Ret_Inh 48.6600606 4.137255e-10 9
## 52 GC_Inh Ret_Inh 0.7478817 8.527122e-01 10
## 53 LivX_Ag Ret_Inh Inf 7.841517e-09 6
## 54 LivX_Inh Ret_Inh 0.7638911 8.047628e-01 7
## 55 AhHyd_Ag Ret_Inh 11.2605735 1.592664e-12 19
## 56 AhHyd_Inh Ret_Inh 2.9433413 3.196646e-04 16
## 57 Thyr_Ag Estr_Ag 419.5878999 6.857653e-05 2
## 58 Thyr_Inh Estr_Ag 0.0000000 1.000000e+00 0
## 59 Ret_Ag Estr_Ag 0.0000000 1.000000e+00 0
## 60 Ret_Inh Estr_Ag 10.6858965 1.283120e-01 1
## 61 Estr_Ag Estr_Ag Inf 2.050117e-12 3
## 62 Estr_Inh Estr_Ag 0.0000000 1.000000e+00 0
## 63 Andr_Ag Estr_Ag 0.0000000 1.000000e+00 0
## 64 Andr_Inh Estr_Ag 369.7264656 4.188769e-03 1
## 65 GC_Ag Estr_Ag 572.4231226 2.724033e-03 1
## 66 GC_Inh Estr_Ag 23.8783153 6.040239e-02 1
## 67 LivX_Ag Estr_Ag 1380.2902407 1.257861e-03 1
## 68 LivX_Inh Estr_Ag 35.0256447 4.177030e-02 1
## 69 AhHyd_Ag Estr_Ag 0.0000000 1.000000e+00 0
## 70 AhHyd_Inh Estr_Ag 53.1252517 2.784157e-02 1
## 71 Thyr_Ag Estr_Inh 160.4688759 1.546010e-33 20
## 72 Thyr_Inh Estr_Inh 113.7475464 6.684890e-50 36
## 73 Ret_Ag Estr_Inh 9.8009726 6.992332e-14 25
## 74 Ret_Inh Estr_Inh 4.6981515 1.652791e-04 10
## 75 Estr_Ag Estr_Inh 0.0000000 1.000000e+00 0
## 76 Estr_Inh Estr_Inh Inf 1.553685e-158 56
## 77 Andr_Ag Estr_Inh 26.6266519 2.784958e-05 4
## 78 Andr_Inh Estr_Inh 195.9290678 3.977371e-15 8
## 79 GC_Ag Estr_Inh 21.5367783 4.973331e-02 1
## 80 GC_Inh Estr_Inh 125.6235132 8.701825e-54 39
## 81 LivX_Ag Estr_Inh 51.6158237 2.326364e-02 1
## 82 LivX_Inh Estr_Inh 69.1183483 6.967515e-34 26
## 83 AhHyd_Ag Estr_Inh 49.1665927 4.027221e-11 8
## 84 AhHyd_Inh Estr_Inh 52.5002742 8.339853e-22 17
## 85 Thyr_Ag Andr_Ag 9.8466778 1.986370e-02 2
## 86 Thyr_Inh Andr_Ag 42.9843963 5.628515e-22 19
## 87 Ret_Ag Andr_Ag 1.4909839 2.675348e-01 5
## 88 Ret_Inh Andr_Ag 2.0897197 1.408049e-01 4
## 89 Estr_Ag Andr_Ag 0.0000000 1.000000e+00 0
## 90 Estr_Inh Andr_Ag 26.6266519 2.784958e-05 4
## 91 Andr_Ag Andr_Ag Inf 1.291057e-131 45
## 92 Andr_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 93 GC_Ag Andr_Ag 26.9525489 4.014828e-02 1
## 94 GC_Inh Andr_Ag 22.5242987 1.660533e-13 14
## 95 LivX_Ag Andr_Ag 0.0000000 1.000000e+00 0
## 96 LivX_Inh Andr_Ag 37.5690728 2.492156e-17 15
## 97 AhHyd_Ag Andr_Ag 12.2268934 1.337955e-02 2
## 98 AhHyd_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 99 Thyr_Ag Andr_Inh 23.5291565 4.118950e-03 2
## 100 Thyr_Inh Andr_Inh 85.7211729 9.704536e-17 12
## 101 Ret_Ag Andr_Inh 5.1257938 3.205604e-03 6
## 102 Ret_Inh Andr_Inh 5.3638099 1.084916e-02 4
## 103 Estr_Ag Andr_Inh 369.7264656 4.188769e-03 1
## 104 Estr_Inh Andr_Inh 195.9290678 3.977371e-15 8
## 105 Andr_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 106 Andr_Inh Andr_Inh Inf 1.914866e-65 20
## 107 GC_Ag Andr_Inh 62.3652674 1.803127e-02 1
## 108 GC_Inh Andr_Inh 60.4186984 3.269870e-14 11
## 109 LivX_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 110 LivX_Inh Andr_Inh 59.5905220 2.742714e-12 9
## 111 AhHyd_Ag Andr_Inh 155.4351087 7.119400e-13 7
## 112 AhHyd_Inh Andr_Inh 353.6544634 2.497908e-27 15
## 113 Thyr_Ag GC_Ag 38.5053671 1.728186e-03 2
## 114 Thyr_Inh GC_Ag 10.0009384 2.201011e-02 2
## 115 Ret_Ag GC_Ag 0.9925479 6.495414e-01 1
## 116 Ret_Inh GC_Ag 48.6600606 4.137255e-10 9
## 117 Estr_Ag GC_Ag 572.4231226 2.724033e-03 1
## 118 Estr_Inh GC_Ag 21.5367783 4.973331e-02 1
## 119 Andr_Ag GC_Ag 26.9525489 4.014828e-02 1
## 120 Andr_Inh GC_Ag 62.3652674 1.803127e-02 1
## 121 GC_Ag GC_Ag Inf 5.960832e-45 13
## 122 GC_Inh GC_Ag 14.4293865 2.109142e-03 3
## 123 LivX_Ag GC_Ag 1338.8541918 1.170823e-08 3
## 124 LivX_Inh GC_Ag 21.2101381 7.147365e-04 3
## 125 AhHyd_Ag GC_Ag 0.0000000 1.000000e+00 0
## 126 AhHyd_Inh GC_Ag 129.2016419 8.850269e-12 7
## 127 Thyr_Ag GC_Inh 62.6810015 9.932654e-45 37
## 128 Thyr_Inh GC_Inh 261.7283374 4.525907e-261 177
## 129 Ret_Ag GC_Inh 8.2914649 1.621225e-51 114
## 130 Ret_Inh GC_Inh 0.7478817 8.527122e-01 10
## 131 Estr_Ag GC_Inh 23.8783153 6.040239e-02 1
## 132 Estr_Inh GC_Inh 125.6235132 8.701825e-54 39
## 133 Andr_Ag GC_Inh 22.5242987 1.660533e-13 14
## 134 Andr_Inh GC_Inh 60.4186984 3.269870e-14 11
## 135 GC_Ag GC_Inh 14.4293865 2.109142e-03 3
## 136 GC_Inh GC_Inh Inf 0.000000e+00 294
## 137 LivX_Ag GC_Inh 23.9557729 5.978819e-03 2
## 138 LivX_Inh GC_Inh 328.9124164 1.370752e-237 155
## 139 AhHyd_Ag GC_Inh 13.4932391 1.131389e-09 12
## 140 AhHyd_Inh GC_Inh 43.4566049 2.156529e-61 57
## 141 Thyr_Ag LivX_Ag 41.7418977 2.859911e-02 1
## 142 Thyr_Inh LivX_Ag 10.9610437 1.030846e-01 1
## 143 Ret_Ag LivX_Ag 0.0000000 1.000000e+00 0
## 144 Ret_Inh LivX_Ag Inf 7.841517e-09 6
## 145 Estr_Ag LivX_Ag 1380.2902407 1.257861e-03 1
## 146 Estr_Inh LivX_Ag 51.6158237 2.326364e-02 1
## 147 Andr_Ag LivX_Ag 0.0000000 1.000000e+00 0
## 148 Andr_Inh LivX_Ag 0.0000000 1.000000e+00 0
## 149 GC_Ag LivX_Ag 1338.8541918 1.170823e-08 3
## 150 GC_Inh LivX_Ag 23.9557729 5.978819e-03 2
## 151 LivX_Ag LivX_Ag Inf 8.411255e-23 6
## 152 LivX_Inh LivX_Ag 14.0229318 8.180412e-02 1
## 153 AhHyd_Ag LivX_Ag 0.0000000 1.000000e+00 0
## 154 AhHyd_Inh LivX_Ag 108.0336487 1.574745e-05 3
## 155 Thyr_Ag LivX_Inh 45.0615986 2.962314e-29 25
## 156 Thyr_Inh LivX_Inh 229.2192571 7.883616e-201 135
## 157 Ret_Ag LivX_Inh 7.4697454 1.471045e-32 75
## 158 Ret_Inh LivX_Inh 0.7638911 8.047628e-01 7
## 159 Estr_Ag LivX_Inh 35.0256447 4.177030e-02 1
## 160 Estr_Inh LivX_Inh 69.1183483 6.967515e-34 26
## 161 Andr_Ag LivX_Inh 37.5690728 2.492156e-17 15
## 162 Andr_Inh LivX_Inh 59.5905220 2.742714e-12 9
## 163 GC_Ag LivX_Inh 21.2101381 7.147365e-04 3
## 164 GC_Inh LivX_Inh 328.9124164 1.370752e-237 155
## 165 LivX_Ag LivX_Inh 14.0229318 8.180412e-02 1
## 166 LivX_Inh LivX_Inh Inf 0.000000e+00 202
## 167 AhHyd_Ag LivX_Inh 10.2925182 1.302391e-05 7
## 168 AhHyd_Inh LivX_Inh 35.2301826 4.722935e-41 39
## 169 Thyr_Ag AhHyd_Ag 21.6994936 7.114372e-06 5
## 170 Thyr_Inh AhHyd_Ag 13.9089778 3.705275e-09 11
## 171 Ret_Ag AhHyd_Ag 3.2725273 1.007141e-03 12
## 172 Ret_Inh AhHyd_Ag 11.2605735 1.592664e-12 19
## 173 Estr_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 174 Estr_Inh AhHyd_Ag 49.1665927 4.027221e-11 8
## 175 Andr_Ag AhHyd_Ag 12.2268934 1.337955e-02 2
## 176 Andr_Inh AhHyd_Ag 155.4351087 7.119400e-13 7
## 177 GC_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 178 GC_Inh AhHyd_Ag 13.4932391 1.131389e-09 12
## 179 LivX_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 180 LivX_Inh AhHyd_Ag 10.2925182 1.302391e-05 7
## 181 AhHyd_Ag AhHyd_Ag Inf 1.553685e-158 56
## 182 AhHyd_Inh AhHyd_Ag 57.6570975 1.493590e-23 18
## 183 Thyr_Ag AhHyd_Inh 16.9176895 1.492924e-08 9
## 184 Thyr_Inh AhHyd_Inh 51.5766435 4.969385e-65 57
## 185 Ret_Ag AhHyd_Inh 5.2194405 3.382033e-14 40
## 186 Ret_Inh AhHyd_Inh 2.9433413 3.196646e-04 16
## 187 Estr_Ag AhHyd_Inh 53.1252517 2.784157e-02 1
## 188 Estr_Inh AhHyd_Inh 52.5002742 8.339853e-22 17
## 189 Andr_Ag AhHyd_Inh 0.0000000 1.000000e+00 0
## 190 Andr_Inh AhHyd_Inh 353.6544634 2.497908e-27 15
## 191 GC_Ag AhHyd_Inh 129.2016419 8.850269e-12 7
## 192 GC_Inh AhHyd_Inh 43.4566049 2.156529e-61 57
## 193 LivX_Ag AhHyd_Inh 108.0336487 1.574745e-05 3
## 194 LivX_Inh AhHyd_Inh 35.2301826 4.722935e-41 39
## 195 AhHyd_Ag AhHyd_Inh 57.6570975 1.493590e-23 18
## 196 AhHyd_Inh AhHyd_Inh Inf 0.000000e+00 134
<- Res
ResMod
$DEGs == ResMod$KBase, ]$OR <- 1
ResMod[ResMod$DEGs == ResMod$KBase, ]$Pval <- 1
ResMod[ResMod
ResMod## DEGs KBase OR Pval Numbers
## 1 Thyr_Ag Thyr_Ag 1.0000000 1.000000e+00 69
## 2 Thyr_Inh Thyr_Ag 47.3899209 1.314468e-34 30
## 3 Ret_Ag Thyr_Ag 13.3903265 2.579072e-22 36
## 4 Ret_Inh Thyr_Ag 2.4260223 3.410822e-02 7
## 5 Estr_Ag Thyr_Ag 419.5878999 6.857653e-05 2
## 6 Estr_Inh Thyr_Ag 160.4688759 1.546010e-33 20
## 7 Andr_Ag Thyr_Ag 9.8466778 1.986370e-02 2
## 8 Andr_Inh Thyr_Ag 23.5291565 4.118950e-03 2
## 9 GC_Ag Thyr_Ag 38.5053671 1.728186e-03 2
## 10 GC_Inh Thyr_Ag 62.6810015 9.932654e-45 37
## 11 LivX_Ag Thyr_Ag 41.7418977 2.859911e-02 1
## 12 LivX_Inh Thyr_Ag 45.0615986 2.962314e-29 25
## 13 AhHyd_Ag Thyr_Ag 21.6994936 7.114372e-06 5
## 14 AhHyd_Inh Thyr_Ag 16.9176895 1.492924e-08 9
## 15 Thyr_Ag Thyr_Inh 47.3899209 1.314468e-34 30
## 16 Thyr_Inh Thyr_Inh 1.0000000 1.000000e+00 257
## 17 Ret_Ag Thyr_Inh 6.0580526 7.151751e-31 83
## 18 Ret_Inh Thyr_Inh 1.0466803 4.818121e-01 12
## 19 Estr_Ag Thyr_Inh 0.0000000 1.000000e+00 0
## 20 Estr_Inh Thyr_Inh 113.7475464 6.684890e-50 36
## 21 Andr_Ag Thyr_Inh 42.9843963 5.628515e-22 19
## 22 Andr_Inh Thyr_Inh 85.7211729 9.704536e-17 12
## 23 GC_Ag Thyr_Inh 10.0009384 2.201011e-02 2
## 24 GC_Inh Thyr_Inh 261.7283374 4.525907e-261 177
## 25 LivX_Ag Thyr_Inh 10.9610437 1.030846e-01 1
## 26 LivX_Inh Thyr_Inh 229.2192571 7.883616e-201 135
## 27 AhHyd_Ag Thyr_Inh 13.9089778 3.705275e-09 11
## 28 AhHyd_Inh Thyr_Inh 51.5766435 4.969385e-65 57
## 29 Thyr_Ag Ret_Ag 13.3903265 2.579072e-22 36
## 30 Thyr_Inh Ret_Ag 6.0580526 7.151751e-31 83
## 31 Ret_Ag Ret_Ag 1.0000000 1.000000e+00 1108
## 32 Ret_Inh Ret_Ag 5.9130615 3.312382e-65 191
## 33 Estr_Ag Ret_Ag 0.0000000 1.000000e+00 0
## 34 Estr_Inh Ret_Ag 9.8009726 6.992332e-14 25
## 35 Andr_Ag Ret_Ag 1.4909839 2.675348e-01 5
## 36 Andr_Inh Ret_Ag 5.1257938 3.205604e-03 6
## 37 GC_Ag Ret_Ag 0.9925479 6.495414e-01 1
## 38 GC_Inh Ret_Ag 8.2914649 1.621225e-51 114
## 39 LivX_Ag Ret_Ag 0.0000000 1.000000e+00 0
## 40 LivX_Inh Ret_Ag 7.4697454 1.471045e-32 75
## 41 AhHyd_Ag Ret_Ag 3.2725273 1.007141e-03 12
## 42 AhHyd_Inh Ret_Ag 5.2194405 3.382033e-14 40
## 43 Thyr_Ag Ret_Inh 2.4260223 3.410822e-02 7
## 44 Thyr_Inh Ret_Inh 1.0466803 4.818121e-01 12
## 45 Ret_Ag Ret_Inh 5.9130615 3.312382e-65 191
## 46 Ret_Inh Ret_Inh 1.0000000 1.000000e+00 640
## 47 Estr_Ag Ret_Inh 10.6858965 1.283120e-01 1
## 48 Estr_Inh Ret_Inh 4.6981515 1.652791e-04 10
## 49 Andr_Ag Ret_Inh 2.0897197 1.408049e-01 4
## 50 Andr_Inh Ret_Inh 5.3638099 1.084916e-02 4
## 51 GC_Ag Ret_Inh 48.6600606 4.137255e-10 9
## 52 GC_Inh Ret_Inh 0.7478817 8.527122e-01 10
## 53 LivX_Ag Ret_Inh Inf 7.841517e-09 6
## 54 LivX_Inh Ret_Inh 0.7638911 8.047628e-01 7
## 55 AhHyd_Ag Ret_Inh 11.2605735 1.592664e-12 19
## 56 AhHyd_Inh Ret_Inh 2.9433413 3.196646e-04 16
## 57 Thyr_Ag Estr_Ag 419.5878999 6.857653e-05 2
## 58 Thyr_Inh Estr_Ag 0.0000000 1.000000e+00 0
## 59 Ret_Ag Estr_Ag 0.0000000 1.000000e+00 0
## 60 Ret_Inh Estr_Ag 10.6858965 1.283120e-01 1
## 61 Estr_Ag Estr_Ag 1.0000000 1.000000e+00 3
## 62 Estr_Inh Estr_Ag 0.0000000 1.000000e+00 0
## 63 Andr_Ag Estr_Ag 0.0000000 1.000000e+00 0
## 64 Andr_Inh Estr_Ag 369.7264656 4.188769e-03 1
## 65 GC_Ag Estr_Ag 572.4231226 2.724033e-03 1
## 66 GC_Inh Estr_Ag 23.8783153 6.040239e-02 1
## 67 LivX_Ag Estr_Ag 1380.2902407 1.257861e-03 1
## 68 LivX_Inh Estr_Ag 35.0256447 4.177030e-02 1
## 69 AhHyd_Ag Estr_Ag 0.0000000 1.000000e+00 0
## 70 AhHyd_Inh Estr_Ag 53.1252517 2.784157e-02 1
## 71 Thyr_Ag Estr_Inh 160.4688759 1.546010e-33 20
## 72 Thyr_Inh Estr_Inh 113.7475464 6.684890e-50 36
## 73 Ret_Ag Estr_Inh 9.8009726 6.992332e-14 25
## 74 Ret_Inh Estr_Inh 4.6981515 1.652791e-04 10
## 75 Estr_Ag Estr_Inh 0.0000000 1.000000e+00 0
## 76 Estr_Inh Estr_Inh 1.0000000 1.000000e+00 56
## 77 Andr_Ag Estr_Inh 26.6266519 2.784958e-05 4
## 78 Andr_Inh Estr_Inh 195.9290678 3.977371e-15 8
## 79 GC_Ag Estr_Inh 21.5367783 4.973331e-02 1
## 80 GC_Inh Estr_Inh 125.6235132 8.701825e-54 39
## 81 LivX_Ag Estr_Inh 51.6158237 2.326364e-02 1
## 82 LivX_Inh Estr_Inh 69.1183483 6.967515e-34 26
## 83 AhHyd_Ag Estr_Inh 49.1665927 4.027221e-11 8
## 84 AhHyd_Inh Estr_Inh 52.5002742 8.339853e-22 17
## 85 Thyr_Ag Andr_Ag 9.8466778 1.986370e-02 2
## 86 Thyr_Inh Andr_Ag 42.9843963 5.628515e-22 19
## 87 Ret_Ag Andr_Ag 1.4909839 2.675348e-01 5
## 88 Ret_Inh Andr_Ag 2.0897197 1.408049e-01 4
## 89 Estr_Ag Andr_Ag 0.0000000 1.000000e+00 0
## 90 Estr_Inh Andr_Ag 26.6266519 2.784958e-05 4
## 91 Andr_Ag Andr_Ag 1.0000000 1.000000e+00 45
## 92 Andr_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 93 GC_Ag Andr_Ag 26.9525489 4.014828e-02 1
## 94 GC_Inh Andr_Ag 22.5242987 1.660533e-13 14
## 95 LivX_Ag Andr_Ag 0.0000000 1.000000e+00 0
## 96 LivX_Inh Andr_Ag 37.5690728 2.492156e-17 15
## 97 AhHyd_Ag Andr_Ag 12.2268934 1.337955e-02 2
## 98 AhHyd_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 99 Thyr_Ag Andr_Inh 23.5291565 4.118950e-03 2
## 100 Thyr_Inh Andr_Inh 85.7211729 9.704536e-17 12
## 101 Ret_Ag Andr_Inh 5.1257938 3.205604e-03 6
## 102 Ret_Inh Andr_Inh 5.3638099 1.084916e-02 4
## 103 Estr_Ag Andr_Inh 369.7264656 4.188769e-03 1
## 104 Estr_Inh Andr_Inh 195.9290678 3.977371e-15 8
## 105 Andr_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 106 Andr_Inh Andr_Inh 1.0000000 1.000000e+00 20
## 107 GC_Ag Andr_Inh 62.3652674 1.803127e-02 1
## 108 GC_Inh Andr_Inh 60.4186984 3.269870e-14 11
## 109 LivX_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 110 LivX_Inh Andr_Inh 59.5905220 2.742714e-12 9
## 111 AhHyd_Ag Andr_Inh 155.4351087 7.119400e-13 7
## 112 AhHyd_Inh Andr_Inh 353.6544634 2.497908e-27 15
## 113 Thyr_Ag GC_Ag 38.5053671 1.728186e-03 2
## 114 Thyr_Inh GC_Ag 10.0009384 2.201011e-02 2
## 115 Ret_Ag GC_Ag 0.9925479 6.495414e-01 1
## 116 Ret_Inh GC_Ag 48.6600606 4.137255e-10 9
## 117 Estr_Ag GC_Ag 572.4231226 2.724033e-03 1
## 118 Estr_Inh GC_Ag 21.5367783 4.973331e-02 1
## 119 Andr_Ag GC_Ag 26.9525489 4.014828e-02 1
## 120 Andr_Inh GC_Ag 62.3652674 1.803127e-02 1
## 121 GC_Ag GC_Ag 1.0000000 1.000000e+00 13
## 122 GC_Inh GC_Ag 14.4293865 2.109142e-03 3
## 123 LivX_Ag GC_Ag 1338.8541918 1.170823e-08 3
## 124 LivX_Inh GC_Ag 21.2101381 7.147365e-04 3
## 125 AhHyd_Ag GC_Ag 0.0000000 1.000000e+00 0
## 126 AhHyd_Inh GC_Ag 129.2016419 8.850269e-12 7
## 127 Thyr_Ag GC_Inh 62.6810015 9.932654e-45 37
## 128 Thyr_Inh GC_Inh 261.7283374 4.525907e-261 177
## 129 Ret_Ag GC_Inh 8.2914649 1.621225e-51 114
## 130 Ret_Inh GC_Inh 0.7478817 8.527122e-01 10
## 131 Estr_Ag GC_Inh 23.8783153 6.040239e-02 1
## 132 Estr_Inh GC_Inh 125.6235132 8.701825e-54 39
## 133 Andr_Ag GC_Inh 22.5242987 1.660533e-13 14
## 134 Andr_Inh GC_Inh 60.4186984 3.269870e-14 11
## 135 GC_Ag GC_Inh 14.4293865 2.109142e-03 3
## 136 GC_Inh GC_Inh 1.0000000 1.000000e+00 294
## 137 LivX_Ag GC_Inh 23.9557729 5.978819e-03 2
## 138 LivX_Inh GC_Inh 328.9124164 1.370752e-237 155
## 139 AhHyd_Ag GC_Inh 13.4932391 1.131389e-09 12
## 140 AhHyd_Inh GC_Inh 43.4566049 2.156529e-61 57
## 141 Thyr_Ag LivX_Ag 41.7418977 2.859911e-02 1
## 142 Thyr_Inh LivX_Ag 10.9610437 1.030846e-01 1
## 143 Ret_Ag LivX_Ag 0.0000000 1.000000e+00 0
## 144 Ret_Inh LivX_Ag Inf 7.841517e-09 6
## 145 Estr_Ag LivX_Ag 1380.2902407 1.257861e-03 1
## 146 Estr_Inh LivX_Ag 51.6158237 2.326364e-02 1
## 147 Andr_Ag LivX_Ag 0.0000000 1.000000e+00 0
## 148 Andr_Inh LivX_Ag 0.0000000 1.000000e+00 0
## 149 GC_Ag LivX_Ag 1338.8541918 1.170823e-08 3
## 150 GC_Inh LivX_Ag 23.9557729 5.978819e-03 2
## 151 LivX_Ag LivX_Ag 1.0000000 1.000000e+00 6
## 152 LivX_Inh LivX_Ag 14.0229318 8.180412e-02 1
## 153 AhHyd_Ag LivX_Ag 0.0000000 1.000000e+00 0
## 154 AhHyd_Inh LivX_Ag 108.0336487 1.574745e-05 3
## 155 Thyr_Ag LivX_Inh 45.0615986 2.962314e-29 25
## 156 Thyr_Inh LivX_Inh 229.2192571 7.883616e-201 135
## 157 Ret_Ag LivX_Inh 7.4697454 1.471045e-32 75
## 158 Ret_Inh LivX_Inh 0.7638911 8.047628e-01 7
## 159 Estr_Ag LivX_Inh 35.0256447 4.177030e-02 1
## 160 Estr_Inh LivX_Inh 69.1183483 6.967515e-34 26
## 161 Andr_Ag LivX_Inh 37.5690728 2.492156e-17 15
## 162 Andr_Inh LivX_Inh 59.5905220 2.742714e-12 9
## 163 GC_Ag LivX_Inh 21.2101381 7.147365e-04 3
## 164 GC_Inh LivX_Inh 328.9124164 1.370752e-237 155
## 165 LivX_Ag LivX_Inh 14.0229318 8.180412e-02 1
## 166 LivX_Inh LivX_Inh 1.0000000 1.000000e+00 202
## 167 AhHyd_Ag LivX_Inh 10.2925182 1.302391e-05 7
## 168 AhHyd_Inh LivX_Inh 35.2301826 4.722935e-41 39
## 169 Thyr_Ag AhHyd_Ag 21.6994936 7.114372e-06 5
## 170 Thyr_Inh AhHyd_Ag 13.9089778 3.705275e-09 11
## 171 Ret_Ag AhHyd_Ag 3.2725273 1.007141e-03 12
## 172 Ret_Inh AhHyd_Ag 11.2605735 1.592664e-12 19
## 173 Estr_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 174 Estr_Inh AhHyd_Ag 49.1665927 4.027221e-11 8
## 175 Andr_Ag AhHyd_Ag 12.2268934 1.337955e-02 2
## 176 Andr_Inh AhHyd_Ag 155.4351087 7.119400e-13 7
## 177 GC_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 178 GC_Inh AhHyd_Ag 13.4932391 1.131389e-09 12
## 179 LivX_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 180 LivX_Inh AhHyd_Ag 10.2925182 1.302391e-05 7
## 181 AhHyd_Ag AhHyd_Ag 1.0000000 1.000000e+00 56
## 182 AhHyd_Inh AhHyd_Ag 57.6570975 1.493590e-23 18
## 183 Thyr_Ag AhHyd_Inh 16.9176895 1.492924e-08 9
## 184 Thyr_Inh AhHyd_Inh 51.5766435 4.969385e-65 57
## 185 Ret_Ag AhHyd_Inh 5.2194405 3.382033e-14 40
## 186 Ret_Inh AhHyd_Inh 2.9433413 3.196646e-04 16
## 187 Estr_Ag AhHyd_Inh 53.1252517 2.784157e-02 1
## 188 Estr_Inh AhHyd_Inh 52.5002742 8.339853e-22 17
## 189 Andr_Ag AhHyd_Inh 0.0000000 1.000000e+00 0
## 190 Andr_Inh AhHyd_Inh 353.6544634 2.497908e-27 15
## 191 GC_Ag AhHyd_Inh 129.2016419 8.850269e-12 7
## 192 GC_Inh AhHyd_Inh 43.4566049 2.156529e-61 57
## 193 LivX_Ag AhHyd_Inh 108.0336487 1.574745e-05 3
## 194 LivX_Inh AhHyd_Inh 35.2301826 4.722935e-41 39
## 195 AhHyd_Ag AhHyd_Inh 57.6570975 1.493590e-23 18
## 196 AhHyd_Inh AhHyd_Inh 1.0000000 1.000000e+00 134
I select as significant overlaps having an OR > 2 and at least 25 overlapping genes. Dots are shown for PVals < 0.01 (set in the plot). Max value in the plot must be set according to minimum PVal to avoid dots not to be shown.
<- viridis::cividis(100)[1:80]
cols <- dplyr::filter(ResMod, OR > 2) %>% dplyr::filter(Numbers > 25)
ResSel min(ResSel$Pval)
## [1] 4.525907e-261
max(ResSel$OR)
## [1] 328.9124
<- ggplot(ResSel, aes(DEGs, KBase, label=Numbers)) +
Dot geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1)) +
ggtitle('Overlap across down-regulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_DownReg.pdf'), width=8, height=8)
<- c('Thyr_Ag', 'Thyr_Inh', 'Ret_Ag', 'Ret_Inh', 'Estr_Ag','Estr_Inh', 'LivX_Ag', 'LivX_Inh')
Path <- ResSel[ResSel$DEGs %in% Path & ResSel$KBase %in% Path, ]
ResPath
ResPath## DEGs KBase OR Pval Numbers
## 1 Thyr_Inh Thyr_Ag 47.389921 1.314468e-34 30
## 2 Ret_Ag Thyr_Ag 13.390327 2.579072e-22 36
## 4 Thyr_Ag Thyr_Inh 47.389921 1.314468e-34 30
## 5 Ret_Ag Thyr_Inh 6.058053 7.151751e-31 83
## 6 Estr_Inh Thyr_Inh 113.747546 6.684890e-50 36
## 8 LivX_Inh Thyr_Inh 229.219257 7.883616e-201 135
## 10 Thyr_Ag Ret_Ag 13.390327 2.579072e-22 36
## 11 Thyr_Inh Ret_Ag 6.058053 7.151751e-31 83
## 12 Ret_Inh Ret_Ag 5.913061 3.312382e-65 191
## 14 LivX_Inh Ret_Ag 7.469745 1.471045e-32 75
## 16 Ret_Ag Ret_Inh 5.913061 3.312382e-65 191
## 17 Thyr_Inh Estr_Inh 113.747546 6.684890e-50 36
## 19 LivX_Inh Estr_Inh 69.118348 6.967515e-34 26
## 26 Thyr_Inh LivX_Inh 229.219257 7.883616e-201 135
## 27 Ret_Ag LivX_Inh 7.469745 1.471045e-32 75
## 28 Estr_Inh LivX_Inh 69.118348 6.967515e-34 26
<- viridis::cividis(100)[1:80]
cols <- dplyr::filter(ResPath, OR > 2) %>% dplyr::filter(Numbers > 25)
ResPath min(ResPath$Pval)
## [1] 7.883616e-201
max(ResPath$OR)
## [1] 229.2193
<- ggplot(ResPath, aes(DEGs, KBase, label=Numbers)) +
Dot geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1))+
ggtitle('Overlap across down-regulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_DownReg_Selected.pdf'), width=8, height=8)
<- list(
DEGs_AgvsInh
Thyr_AgvsInh_Up= row.names(DEA$Thyr$AgvsInh$DEGs[DEA$Thyr$AgvsInh$DEGs$log2FoldChange > 0, ]),
Thyr_AgvsInh_Down= row.names(DEA$Thyr$AgvsInh$DEGs[DEA$Thyr$AgvsInh$DEGs$log2FoldChange < 0, ]),
Ret_AgvsInh_Up= row.names(DEA$Ret$AgvsInh$DEGs[DEA$Ret$AgvsInh$DEGs$log2FoldChange > 0, ]),
Ret_AgvsInh_Down= row.names(DEA$Ret$AgvsInh$DEGs[DEA$Ret$AgvsInh$DEGs$log2FoldChange < 0, ]),
Estr_AgvsInh_Up= row.names(DEA$Estr$AgvsInh$DEGs[DEA$Estr$AgvsInh$DEGs$log2FoldChange > 0, ]),
Estr_AgvsInh_Down= row.names(DEA$Estr$AgvsInh$DEGs[DEA$Estr$AgvsInh$DEGs$log2FoldChange < 0, ]),
Andr_AgvsInh_Up= row.names(DEA$Andr$AgvsInh$DEGs[DEA$Andr$AgvsInh$DEGs$log2FoldChange > 0, ]),
Andr_AgvsInh_Down= row.names(DEA$Andr$AgvsInh$DEGs[DEA$Andr$AgvsInh$DEGs$log2FoldChange < 0, ]),
GC_AgvsInh_Up= row.names(DEA$GC$AgvsInh$DEGs[DEA$GC$AgvsInh$DEGs$log2FoldChange > 0, ]),
GC_AgvsInh_Down= row.names(DEA$GC$AgvsInh$DEGs[DEA$GC$AgvsInh$DEGs$log2FoldChange < 0, ]),
LivX_AgvsInh_Up= row.names(DEA$LivX$AgvsInh$DEGs[DEA$LivX$AgvsInh$DEGs$log2FoldChange > 0, ]),
LivX_AgvsInh_Down= row.names(DEA$LivX$AgvsInh$DEGs[DEA$LivX$AgvsInh$DEGs$log2FoldChange < 0, ]),
AhHyd_AgvsInh_Up= row.names(DEA$AhHyd$AgvsInh$DEGs[DEA$AhHyd$AgvsInh$DEGs$log2FoldChange > 0, ]),
AhHyd_AgvsInh_Down= row.names(DEA$AhHyd$AgvsInh$DEGs[DEA$AhHyd$AgvsInh$DEGs$log2FoldChange < 0, ])
)
<- row.names(DEA$Ret$Agonist$Res) %>% unique()
Universe length(Universe)
## [1] 14305
<- newGOM(DEGs_AgvsInh, DEGs_AgvsInh, genome.size=length(Universe))
OvObj #print(OvObj)
getMatrix(OvObj, name='intersection')
## Thyr_AgvsInh_Up Thyr_AgvsInh_Down Ret_AgvsInh_Up
## Thyr_AgvsInh_Up 191 0 79
## Thyr_AgvsInh_Down 0 133 35
## Ret_AgvsInh_Up 79 35 2171
## Ret_AgvsInh_Down 45 24 0
## Estr_AgvsInh_Up 8 1 11
## Estr_AgvsInh_Down 0 13 3
## Andr_AgvsInh_Up 4 77 97
## Andr_AgvsInh_Down 27 3 46
## GC_AgvsInh_Up 85 0 29
## GC_AgvsInh_Down 0 63 75
## LivX_AgvsInh_Up 67 1 29
## LivX_AgvsInh_Down 1 60 103
## AhHyd_AgvsInh_Up 8 18 41
## AhHyd_AgvsInh_Down 11 4 172
## Ret_AgvsInh_Down Estr_AgvsInh_Up Estr_AgvsInh_Down
## Thyr_AgvsInh_Up 45 8 0
## Thyr_AgvsInh_Down 24 1 13
## Ret_AgvsInh_Up 0 11 3
## Ret_AgvsInh_Down 1370 11 4
## Estr_AgvsInh_Up 11 32 0
## Estr_AgvsInh_Down 4 0 26
## Andr_AgvsInh_Up 18 4 11
## Andr_AgvsInh_Down 89 2 3
## GC_AgvsInh_Up 167 18 3
## GC_AgvsInh_Down 14 0 12
## LivX_AgvsInh_Up 129 11 2
## LivX_AgvsInh_Down 12 0 14
## AhHyd_AgvsInh_Up 18 3 3
## AhHyd_AgvsInh_Down 31 1 2
## Andr_AgvsInh_Up Andr_AgvsInh_Down GC_AgvsInh_Up
## Thyr_AgvsInh_Up 4 27 85
## Thyr_AgvsInh_Down 77 3 0
## Ret_AgvsInh_Up 97 46 29
## Ret_AgvsInh_Down 18 89 167
## Estr_AgvsInh_Up 4 2 18
## Estr_AgvsInh_Down 11 3 3
## Andr_AgvsInh_Up 325 0 4
## Andr_AgvsInh_Down 0 225 66
## GC_AgvsInh_Up 4 66 373
## GC_AgvsInh_Down 90 5 0
## LivX_AgvsInh_Up 1 49 198
## LivX_AgvsInh_Down 80 11 0
## AhHyd_AgvsInh_Up 44 0 9
## AhHyd_AgvsInh_Down 0 59 26
## GC_AgvsInh_Down LivX_AgvsInh_Up LivX_AgvsInh_Down
## Thyr_AgvsInh_Up 0 67 1
## Thyr_AgvsInh_Down 63 1 60
## Ret_AgvsInh_Up 75 29 103
## Ret_AgvsInh_Down 14 129 12
## Estr_AgvsInh_Up 0 11 0
## Estr_AgvsInh_Down 12 2 14
## Andr_AgvsInh_Up 90 1 80
## Andr_AgvsInh_Down 5 49 11
## GC_AgvsInh_Up 0 198 0
## GC_AgvsInh_Down 171 0 117
## LivX_AgvsInh_Up 0 291 0
## LivX_AgvsInh_Down 117 0 192
## AhHyd_AgvsInh_Up 31 8 29
## AhHyd_AgvsInh_Down 10 21 17
## AhHyd_AgvsInh_Up AhHyd_AgvsInh_Down
## Thyr_AgvsInh_Up 8 11
## Thyr_AgvsInh_Down 18 4
## Ret_AgvsInh_Up 41 172
## Ret_AgvsInh_Down 18 31
## Estr_AgvsInh_Up 3 1
## Estr_AgvsInh_Down 3 2
## Andr_AgvsInh_Up 44 0
## Andr_AgvsInh_Down 0 59
## GC_AgvsInh_Up 9 26
## GC_AgvsInh_Down 31 10
## LivX_AgvsInh_Up 8 21
## LivX_AgvsInh_Down 29 17
## AhHyd_AgvsInh_Up 110 0
## AhHyd_AgvsInh_Down 0 280
getMatrix(OvObj, name='pval')
## Thyr_AgvsInh_Up Thyr_AgvsInh_Down Ret_AgvsInh_Up
## Thyr_AgvsInh_Up 0.000000e+00 1.000000e+00 1.421630e-18
## Thyr_AgvsInh_Down 1.000000e+00 0.000000e+00 5.901433e-04
## Ret_AgvsInh_Up 1.421630e-18 5.901433e-04 0.000000e+00
## Ret_AgvsInh_Down 8.726946e-09 1.731715e-03 1.000000e+00
## Estr_AgvsInh_Up 6.974103e-09 2.586155e-01 5.653845e-03
## Estr_AgvsInh_Down 1.000000e+00 1.999327e-20 7.778992e-01
## Andr_AgvsInh_Up 6.342118e-01 1.019081e-93 8.941044e-12
## Andr_AgvsInh_Down 2.322727e-18 3.484756e-01 1.956813e-02
## GC_AgvsInh_Up 6.298575e-85 1.000000e+00 9.999957e-01
## GC_AgvsInh_Down 1.000000e+00 6.364375e-89 1.791092e-19
## LivX_AgvsInh_Up 6.733621e-66 9.358337e-01 9.966646e-01
## LivX_AgvsInh_Down 9.256038e-01 3.444565e-79 1.135165e-35
## AhHyd_AgvsInh_Up 1.118496e-04 8.043640e-18 1.043005e-08
## AhHyd_AgvsInh_Down 1.367533e-03 2.634182e-01 1.681532e-71
## Ret_AgvsInh_Down Estr_AgvsInh_Up Estr_AgvsInh_Down
## Thyr_AgvsInh_Up 8.726946e-09 6.974103e-09 1.000000e+00
## Thyr_AgvsInh_Down 1.731715e-03 2.586155e-01 1.999327e-20
## Ret_AgvsInh_Up 1.000000e+00 5.653845e-03 7.778992e-01
## Ret_AgvsInh_Down 0.000000e+00 1.154895e-04 2.343454e-01
## Estr_AgvsInh_Up 1.154895e-04 2.881573e-98 1.000000e+00
## Estr_AgvsInh_Down 2.343454e-01 1.000000e+00 3.739447e-82
## Andr_AgvsInh_Up 9.972662e-01 5.693650e-03 4.010907e-12
## Andr_AgvsInh_Down 9.213323e-34 8.982384e-02 7.644201e-03
## GC_AgvsInh_Up 5.706244e-73 6.985781e-21 2.933257e-02
## GC_AgvsInh_Down 7.694561e-01 1.000000e+00 4.816229e-17
## LivX_AgvsInh_Up 1.435075e-55 1.805373e-11 9.741783e-02
## LivX_AgvsInh_Down 9.622804e-01 1.000000e+00 3.200680e-20
## AhHyd_AgvsInh_Up 1.660658e-02 1.865553e-03 1.011205e-03
## AhHyd_AgvsInh_Down 2.214766e-01 4.691410e-01 9.126644e-02
## Andr_AgvsInh_Up Andr_AgvsInh_Down GC_AgvsInh_Up
## Thyr_AgvsInh_Up 6.342118e-01 2.322727e-18 6.298575e-85
## Thyr_AgvsInh_Down 1.019081e-93 3.484756e-01 1.000000e+00
## Ret_AgvsInh_Up 8.941044e-12 1.956813e-02 9.999957e-01
## Ret_AgvsInh_Down 9.972662e-01 9.213323e-34 5.706244e-73
## Estr_AgvsInh_Up 5.693650e-03 8.982384e-02 6.985781e-21
## Estr_AgvsInh_Down 4.010907e-12 7.644201e-03 2.933257e-02
## Andr_AgvsInh_Up 0.000000e+00 1.000000e+00 9.721261e-01
## Andr_AgvsInh_Down 1.000000e+00 0.000000e+00 1.917203e-51
## GC_AgvsInh_Up 9.721261e-01 1.917203e-51 0.000000e+00
## GC_AgvsInh_Down 7.080601e-105 1.328217e-01 1.000000e+00
## LivX_AgvsInh_Up 9.988374e-01 1.038155e-36 1.198721e-264
## LivX_AgvsInh_Down 3.577890e-82 2.313084e-04 1.000000e+00
## AhHyd_AgvsInh_Up 7.366421e-44 1.000000e+00 2.319710e-03
## AhHyd_AgvsInh_Down 1.000000e+00 1.946507e-50 2.103207e-08
## GC_AgvsInh_Down LivX_AgvsInh_Up LivX_AgvsInh_Down
## Thyr_AgvsInh_Up 1.000000e+00 6.733621e-66 9.256038e-01
## Thyr_AgvsInh_Down 6.364375e-89 9.358337e-01 3.444565e-79
## Ret_AgvsInh_Up 1.791092e-19 9.966646e-01 1.135165e-35
## Ret_AgvsInh_Down 7.694561e-01 1.435075e-55 9.622804e-01
## Estr_AgvsInh_Up 1.000000e+00 1.805373e-11 1.000000e+00
## Estr_AgvsInh_Down 4.816229e-17 9.741783e-02 3.200680e-20
## Andr_AgvsInh_Up 7.080601e-105 9.988374e-01 3.577890e-82
## Andr_AgvsInh_Down 1.328217e-01 1.038155e-36 2.313084e-04
## GC_AgvsInh_Up 1.000000e+00 1.198721e-264 1.000000e+00
## GC_AgvsInh_Down 0.000000e+00 1.000000e+00 1.507718e-194
## LivX_AgvsInh_Up 1.000000e+00 0.000000e+00 1.000000e+00
## LivX_AgvsInh_Down 1.507718e-194 1.000000e+00 0.000000e+00
## AhHyd_AgvsInh_Up 1.460928e-34 1.817733e-03 7.100713e-30
## AhHyd_AgvsInh_Down 1.997478e-03 2.855977e-07 2.302002e-07
## AhHyd_AgvsInh_Up AhHyd_AgvsInh_Down
## Thyr_AgvsInh_Up 1.118496e-04 1.367533e-03
## Thyr_AgvsInh_Down 8.043640e-18 2.634182e-01
## Ret_AgvsInh_Up 1.043005e-08 1.681532e-71
## Ret_AgvsInh_Down 1.660658e-02 2.214766e-01
## Estr_AgvsInh_Up 1.865553e-03 4.691410e-01
## Estr_AgvsInh_Down 1.011205e-03 9.126644e-02
## Andr_AgvsInh_Up 7.366421e-44 1.000000e+00
## Andr_AgvsInh_Down 1.000000e+00 1.946507e-50
## GC_AgvsInh_Up 2.319710e-03 2.103207e-08
## GC_AgvsInh_Down 1.460928e-34 1.997478e-03
## LivX_AgvsInh_Up 1.817733e-03 2.855977e-07
## LivX_AgvsInh_Down 7.100713e-30 2.302002e-07
## AhHyd_AgvsInh_Up 1.904254e-279 1.000000e+00
## AhHyd_AgvsInh_Down 1.000000e+00 0.000000e+00
getMatrix(OvObj, name='odds.ratio')
## Thyr_AgvsInh_Up Thyr_AgvsInh_Down Ret_AgvsInh_Up
## Thyr_AgvsInh_Up Inf 0.0000000 4.0530055
## Thyr_AgvsInh_Down 0.0000000 Inf 2.0123753
## Ret_AgvsInh_Up 4.0530055 2.0123753 Inf
## Ret_AgvsInh_Down 2.9744832 2.0979815 0.0000000
## Estr_AgvsInh_Up 25.6461692 3.4551786 2.9371490
## Estr_AgvsInh_Down 0.0000000 117.3982815 0.7286571
## Andr_AgvsInh_Up 0.9191247 76.9388578 2.4419925
## Andr_AgvsInh_Down 11.5631303 1.4500290 1.4457123
## GC_AgvsInh_Up 38.4467168 0.0000000 0.4640398
## GC_AgvsInh_Down 0.0000000 116.7920632 4.4865051
## LivX_AgvsInh_Up 33.4636059 0.3626601 0.6135011
## LivX_AgvsInh_Down 0.3836762 87.1889226 6.7392307
## AhHyd_AgvsInh_Up 6.0033903 23.9241607 3.3653543
## AhHyd_AgvsInh_Down 3.1448076 1.5610879 9.5782571
## Ret_AgvsInh_Down Estr_AgvsInh_Up Estr_AgvsInh_Down
## Thyr_AgvsInh_Up 2.9744832 25.646169 0.0000000
## Thyr_AgvsInh_Down 2.0979815 3.455179 117.3982815
## Ret_AgvsInh_Up 0.0000000 2.937149 0.7286571
## Ret_AgvsInh_Down Inf 4.976574 1.7186678
## Estr_AgvsInh_Up 4.9765736 Inf 0.0000000
## Estr_AgvsInh_Down 1.7186678 0.000000 Inf
## Andr_AgvsInh_Up 0.5476547 6.207121 32.5542122
## Andr_AgvsInh_Down 6.5365413 4.199557 8.2554654
## GC_AgvsInh_Up 8.5752537 50.396915 4.9025775
## GC_AgvsInh_Down 0.8402834 0.000000 75.8000556
## LivX_AgvsInh_Up 8.1934729 26.144914 4.0332363
## LivX_AgvsInh_Down 0.6261832 0.000000 92.0962413
## AhHyd_AgvsInh_Up 1.8583830 13.690359 17.2593505
## AhHyd_AgvsInh_Down 1.1795080 1.617904 4.1955388
## Andr_AgvsInh_Up Andr_AgvsInh_Down GC_AgvsInh_Up
## Thyr_AgvsInh_Up 0.9191247 11.563130 38.4467168
## Thyr_AgvsInh_Down 76.9388578 1.450029 0.0000000
## Ret_AgvsInh_Up 2.4419925 1.445712 0.4640398
## Ret_AgvsInh_Down 0.5476547 6.536541 8.5752537
## Estr_AgvsInh_Up 6.2071211 4.199557 50.3969154
## Estr_AgvsInh_Down 32.5542122 8.255465 4.9025775
## Andr_AgvsInh_Up Inf 0.000000 0.4596587
## Andr_AgvsInh_Down 0.0000000 Inf 18.6084381
## GC_AgvsInh_Up 0.4596587 18.608438 Inf
## GC_AgvsInh_Down 65.5910019 1.904881 0.0000000
## LivX_AgvsInh_Up 0.1456846 15.909984 168.1952201
## LivX_AgvsInh_Down 40.3770388 3.946417 0.0000000
## AhHyd_AgvsInh_Up 32.9806140 0.000000 3.3853489
## AhHyd_AgvsInh_Down 0.0000000 22.281218 4.0341595
## GC_AgvsInh_Down LivX_AgvsInh_Up LivX_AgvsInh_Down
## Thyr_AgvsInh_Up 0.0000000 33.4636059 0.3836762
## Thyr_AgvsInh_Down 116.7920632 0.3626601 87.1889226
## Ret_AgvsInh_Up 4.4865051 0.6135011 6.7392307
## Ret_AgvsInh_Down 0.8402834 8.1934729 0.6261832
## Estr_AgvsInh_Up 0.0000000 26.1449143 0.0000000
## Estr_AgvsInh_Down 75.8000556 4.0332363 92.0962413
## Andr_AgvsInh_Up 65.5910019 0.1456846 40.3770388
## Andr_AgvsInh_Down 1.9048813 15.9099839 3.9464174
## GC_AgvsInh_Up 0.0000000 168.1952201 0.0000000
## GC_AgvsInh_Down Inf 0.0000000 405.5958594
## LivX_AgvsInh_Up 0.0000000 Inf 0.0000000
## LivX_AgvsInh_Down 405.5958594 0.0000000 Inf
## AhHyd_AgvsInh_Up 39.3284554 3.8549883 30.7704613
## AhHyd_AgvsInh_Down 3.1888304 4.1298212 5.1142504
## AhHyd_AgvsInh_Up AhHyd_AgvsInh_Down
## Thyr_AgvsInh_Up 6.003390 3.144808
## Thyr_AgvsInh_Down 23.924161 1.561088
## Ret_AgvsInh_Up 3.365354 9.578257
## Ret_AgvsInh_Down 1.858383 1.179508
## Estr_AgvsInh_Up 13.690359 1.617904
## Estr_AgvsInh_Down 17.259351 4.195539
## Andr_AgvsInh_Up 32.980614 0.000000
## Andr_AgvsInh_Down 0.000000 22.281218
## GC_AgvsInh_Up 3.385349 4.034159
## GC_AgvsInh_Down 39.328455 3.188830
## LivX_AgvsInh_Up 3.854988 4.129821
## LivX_AgvsInh_Down 30.770461 5.114250
## AhHyd_AgvsInh_Up Inf 0.000000
## AhHyd_AgvsInh_Down 0.000000 Inf
DotPlot: data preparation
<- data.frame(getMatrix(OvObj, name='odds.ratio'))
OR $DEGs <- row.names(OR)
OR<- gather(OR, 'KBase', 'OR', -DEGs)
OR <- data.frame(getMatrix(OvObj, name='pval'))
PVAL $DEGs <- row.names(PVAL)
PVAL<- gather(PVAL, 'KBase', 'PVal', -DEGs)
PVAL <- data.frame(getMatrix(OvObj, name='intersection'))
NUM $DEGs <- row.names(NUM)
NUM<- gather(NUM, 'KBase', 'Numbers', -DEGs)
NUM if(! identical(OR$DEGs, PVAL$DEGs)){
stop('Inconsistecy')
}if(! identical(OR$DEGs, NUM$DEGs)){
stop('Inconsistecy')
}if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}<- mutate(OR, Pval=PVAL$PVal) %>% mutate(Numbers=NUM$Numbers)
Res
Res## DEGs KBase OR Pval Numbers
## 1 Thyr_AgvsInh_Up Thyr_AgvsInh_Up Inf 0.000000e+00 191
## 2 Thyr_AgvsInh_Down Thyr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 3 Ret_AgvsInh_Up Thyr_AgvsInh_Up 4.0530055 1.421630e-18 79
## 4 Ret_AgvsInh_Down Thyr_AgvsInh_Up 2.9744832 8.726946e-09 45
## 5 Estr_AgvsInh_Up Thyr_AgvsInh_Up 25.6461692 6.974103e-09 8
## 6 Estr_AgvsInh_Down Thyr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 7 Andr_AgvsInh_Up Thyr_AgvsInh_Up 0.9191247 6.342118e-01 4
## 8 Andr_AgvsInh_Down Thyr_AgvsInh_Up 11.5631303 2.322727e-18 27
## 9 GC_AgvsInh_Up Thyr_AgvsInh_Up 38.4467168 6.298575e-85 85
## 10 GC_AgvsInh_Down Thyr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 11 LivX_AgvsInh_Up Thyr_AgvsInh_Up 33.4636059 6.733621e-66 67
## 12 LivX_AgvsInh_Down Thyr_AgvsInh_Up 0.3836762 9.256038e-01 1
## 13 AhHyd_AgvsInh_Up Thyr_AgvsInh_Up 6.0033903 1.118496e-04 8
## 14 AhHyd_AgvsInh_Down Thyr_AgvsInh_Up 3.1448076 1.367533e-03 11
## 15 Thyr_AgvsInh_Up Thyr_AgvsInh_Down 0.0000000 1.000000e+00 0
## 16 Thyr_AgvsInh_Down Thyr_AgvsInh_Down Inf 0.000000e+00 133
## 17 Ret_AgvsInh_Up Thyr_AgvsInh_Down 2.0123753 5.901433e-04 35
## 18 Ret_AgvsInh_Down Thyr_AgvsInh_Down 2.0979815 1.731715e-03 24
## 19 Estr_AgvsInh_Up Thyr_AgvsInh_Down 3.4551786 2.586155e-01 1
## 20 Estr_AgvsInh_Down Thyr_AgvsInh_Down 117.3982815 1.999327e-20 13
## 21 Andr_AgvsInh_Up Thyr_AgvsInh_Down 76.9388578 1.019081e-93 77
## 22 Andr_AgvsInh_Down Thyr_AgvsInh_Down 1.4500290 3.484756e-01 3
## 23 GC_AgvsInh_Up Thyr_AgvsInh_Down 0.0000000 1.000000e+00 0
## 24 GC_AgvsInh_Down Thyr_AgvsInh_Down 116.7920632 6.364375e-89 63
## 25 LivX_AgvsInh_Up Thyr_AgvsInh_Down 0.3626601 9.358337e-01 1
## 26 LivX_AgvsInh_Down Thyr_AgvsInh_Down 87.1889226 3.444565e-79 60
## 27 AhHyd_AgvsInh_Up Thyr_AgvsInh_Down 23.9241607 8.043640e-18 18
## 28 AhHyd_AgvsInh_Down Thyr_AgvsInh_Down 1.5610879 2.634182e-01 4
## 29 Thyr_AgvsInh_Up Ret_AgvsInh_Up 4.0530055 1.421630e-18 79
## 30 Thyr_AgvsInh_Down Ret_AgvsInh_Up 2.0123753 5.901433e-04 35
## 31 Ret_AgvsInh_Up Ret_AgvsInh_Up Inf 0.000000e+00 2171
## 32 Ret_AgvsInh_Down Ret_AgvsInh_Up 0.0000000 1.000000e+00 0
## 33 Estr_AgvsInh_Up Ret_AgvsInh_Up 2.9371490 5.653845e-03 11
## 34 Estr_AgvsInh_Down Ret_AgvsInh_Up 0.7286571 7.778992e-01 3
## 35 Andr_AgvsInh_Up Ret_AgvsInh_Up 2.4419925 8.941044e-12 97
## 36 Andr_AgvsInh_Down Ret_AgvsInh_Up 1.4457123 1.956813e-02 46
## 37 GC_AgvsInh_Up Ret_AgvsInh_Up 0.4640398 9.999957e-01 29
## 38 GC_AgvsInh_Down Ret_AgvsInh_Up 4.4865051 1.791092e-19 75
## 39 LivX_AgvsInh_Up Ret_AgvsInh_Up 0.6135011 9.966646e-01 29
## 40 LivX_AgvsInh_Down Ret_AgvsInh_Up 6.7392307 1.135165e-35 103
## 41 AhHyd_AgvsInh_Up Ret_AgvsInh_Up 3.3653543 1.043005e-08 41
## 42 AhHyd_AgvsInh_Down Ret_AgvsInh_Up 9.5782571 1.681532e-71 172
## 43 Thyr_AgvsInh_Up Ret_AgvsInh_Down 2.9744832 8.726946e-09 45
## 44 Thyr_AgvsInh_Down Ret_AgvsInh_Down 2.0979815 1.731715e-03 24
## 45 Ret_AgvsInh_Up Ret_AgvsInh_Down 0.0000000 1.000000e+00 0
## 46 Ret_AgvsInh_Down Ret_AgvsInh_Down Inf 0.000000e+00 1370
## 47 Estr_AgvsInh_Up Ret_AgvsInh_Down 4.9765736 1.154895e-04 11
## 48 Estr_AgvsInh_Down Ret_AgvsInh_Down 1.7186678 2.343454e-01 4
## 49 Andr_AgvsInh_Up Ret_AgvsInh_Down 0.5476547 9.972662e-01 18
## 50 Andr_AgvsInh_Down Ret_AgvsInh_Down 6.5365413 9.213323e-34 89
## 51 GC_AgvsInh_Up Ret_AgvsInh_Down 8.5752537 5.706244e-73 167
## 52 GC_AgvsInh_Down Ret_AgvsInh_Down 0.8402834 7.694561e-01 14
## 53 LivX_AgvsInh_Up Ret_AgvsInh_Down 8.1934729 1.435075e-55 129
## 54 LivX_AgvsInh_Down Ret_AgvsInh_Down 0.6261832 9.622804e-01 12
## 55 AhHyd_AgvsInh_Up Ret_AgvsInh_Down 1.8583830 1.660658e-02 18
## 56 AhHyd_AgvsInh_Down Ret_AgvsInh_Down 1.1795080 2.214766e-01 31
## 57 Thyr_AgvsInh_Up Estr_AgvsInh_Up 25.6461692 6.974103e-09 8
## 58 Thyr_AgvsInh_Down Estr_AgvsInh_Up 3.4551786 2.586155e-01 1
## 59 Ret_AgvsInh_Up Estr_AgvsInh_Up 2.9371490 5.653845e-03 11
## 60 Ret_AgvsInh_Down Estr_AgvsInh_Up 4.9765736 1.154895e-04 11
## 61 Estr_AgvsInh_Up Estr_AgvsInh_Up Inf 2.881573e-98 32
## 62 Estr_AgvsInh_Down Estr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 63 Andr_AgvsInh_Up Estr_AgvsInh_Up 6.2071211 5.693650e-03 4
## 64 Andr_AgvsInh_Down Estr_AgvsInh_Up 4.1995573 8.982384e-02 2
## 65 GC_AgvsInh_Up Estr_AgvsInh_Up 50.3969154 6.985781e-21 18
## 66 GC_AgvsInh_Down Estr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 67 LivX_AgvsInh_Up Estr_AgvsInh_Up 26.1449143 1.805373e-11 11
## 68 LivX_AgvsInh_Down Estr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 69 AhHyd_AgvsInh_Up Estr_AgvsInh_Up 13.6903593 1.865553e-03 3
## 70 AhHyd_AgvsInh_Down Estr_AgvsInh_Up 1.6179044 4.691410e-01 1
## 71 Thyr_AgvsInh_Up Estr_AgvsInh_Down 0.0000000 1.000000e+00 0
## 72 Thyr_AgvsInh_Down Estr_AgvsInh_Down 117.3982815 1.999327e-20 13
## 73 Ret_AgvsInh_Up Estr_AgvsInh_Down 0.7286571 7.778992e-01 3
## 74 Ret_AgvsInh_Down Estr_AgvsInh_Down 1.7186678 2.343454e-01 4
## 75 Estr_AgvsInh_Up Estr_AgvsInh_Down 0.0000000 1.000000e+00 0
## 76 Estr_AgvsInh_Down Estr_AgvsInh_Down Inf 3.739447e-82 26
## 77 Andr_AgvsInh_Up Estr_AgvsInh_Down 32.5542122 4.010907e-12 11
## 78 Andr_AgvsInh_Down Estr_AgvsInh_Down 8.2554654 7.644201e-03 3
## 79 GC_AgvsInh_Up Estr_AgvsInh_Down 4.9025775 2.933257e-02 3
## 80 GC_AgvsInh_Down Estr_AgvsInh_Down 75.8000556 4.816229e-17 12
## 81 LivX_AgvsInh_Up Estr_AgvsInh_Down 4.0332363 9.741783e-02 2
## 82 LivX_AgvsInh_Down Estr_AgvsInh_Down 92.0962413 3.200680e-20 14
## 83 AhHyd_AgvsInh_Up Estr_AgvsInh_Down 17.2593505 1.011205e-03 3
## 84 AhHyd_AgvsInh_Down Estr_AgvsInh_Down 4.1955388 9.126644e-02 2
## 85 Thyr_AgvsInh_Up Andr_AgvsInh_Up 0.9191247 6.342118e-01 4
## 86 Thyr_AgvsInh_Down Andr_AgvsInh_Up 76.9388578 1.019081e-93 77
## 87 Ret_AgvsInh_Up Andr_AgvsInh_Up 2.4419925 8.941044e-12 97
## 88 Ret_AgvsInh_Down Andr_AgvsInh_Up 0.5476547 9.972662e-01 18
## 89 Estr_AgvsInh_Up Andr_AgvsInh_Up 6.2071211 5.693650e-03 4
## 90 Estr_AgvsInh_Down Andr_AgvsInh_Up 32.5542122 4.010907e-12 11
## 91 Andr_AgvsInh_Up Andr_AgvsInh_Up Inf 0.000000e+00 325
## 92 Andr_AgvsInh_Down Andr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 93 GC_AgvsInh_Up Andr_AgvsInh_Up 0.4596587 9.721261e-01 4
## 94 GC_AgvsInh_Down Andr_AgvsInh_Up 65.5910019 7.080601e-105 90
## 95 LivX_AgvsInh_Up Andr_AgvsInh_Up 0.1456846 9.988374e-01 1
## 96 LivX_AgvsInh_Down Andr_AgvsInh_Up 40.3770388 3.577890e-82 80
## 97 AhHyd_AgvsInh_Up Andr_AgvsInh_Up 32.9806140 7.366421e-44 44
## 98 AhHyd_AgvsInh_Down Andr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 99 Thyr_AgvsInh_Up Andr_AgvsInh_Down 11.5631303 2.322727e-18 27
## 100 Thyr_AgvsInh_Down Andr_AgvsInh_Down 1.4500290 3.484756e-01 3
## 101 Ret_AgvsInh_Up Andr_AgvsInh_Down 1.4457123 1.956813e-02 46
## 102 Ret_AgvsInh_Down Andr_AgvsInh_Down 6.5365413 9.213323e-34 89
## 103 Estr_AgvsInh_Up Andr_AgvsInh_Down 4.1995573 8.982384e-02 2
## 104 Estr_AgvsInh_Down Andr_AgvsInh_Down 8.2554654 7.644201e-03 3
## 105 Andr_AgvsInh_Up Andr_AgvsInh_Down 0.0000000 1.000000e+00 0
## 106 Andr_AgvsInh_Down Andr_AgvsInh_Down Inf 0.000000e+00 225
## 107 GC_AgvsInh_Up Andr_AgvsInh_Down 18.6084381 1.917203e-51 66
## 108 GC_AgvsInh_Down Andr_AgvsInh_Down 1.9048813 1.328217e-01 5
## 109 LivX_AgvsInh_Up Andr_AgvsInh_Down 15.9099839 1.038155e-36 49
## 110 LivX_AgvsInh_Down Andr_AgvsInh_Down 3.9464174 2.313084e-04 11
## 111 AhHyd_AgvsInh_Up Andr_AgvsInh_Down 0.0000000 1.000000e+00 0
## 112 AhHyd_AgvsInh_Down Andr_AgvsInh_Down 22.2812178 1.946507e-50 59
## 113 Thyr_AgvsInh_Up GC_AgvsInh_Up 38.4467168 6.298575e-85 85
## 114 Thyr_AgvsInh_Down GC_AgvsInh_Up 0.0000000 1.000000e+00 0
## 115 Ret_AgvsInh_Up GC_AgvsInh_Up 0.4640398 9.999957e-01 29
## 116 Ret_AgvsInh_Down GC_AgvsInh_Up 8.5752537 5.706244e-73 167
## 117 Estr_AgvsInh_Up GC_AgvsInh_Up 50.3969154 6.985781e-21 18
## 118 Estr_AgvsInh_Down GC_AgvsInh_Up 4.9025775 2.933257e-02 3
## 119 Andr_AgvsInh_Up GC_AgvsInh_Up 0.4596587 9.721261e-01 4
## 120 Andr_AgvsInh_Down GC_AgvsInh_Up 18.6084381 1.917203e-51 66
## 121 GC_AgvsInh_Up GC_AgvsInh_Up Inf 0.000000e+00 373
## 122 GC_AgvsInh_Down GC_AgvsInh_Up 0.0000000 1.000000e+00 0
## 123 LivX_AgvsInh_Up GC_AgvsInh_Up 168.1952201 1.198721e-264 198
## 124 LivX_AgvsInh_Down GC_AgvsInh_Up 0.0000000 1.000000e+00 0
## 125 AhHyd_AgvsInh_Up GC_AgvsInh_Up 3.3853489 2.319710e-03 9
## 126 AhHyd_AgvsInh_Down GC_AgvsInh_Up 4.0341595 2.103207e-08 26
## 127 Thyr_AgvsInh_Up GC_AgvsInh_Down 0.0000000 1.000000e+00 0
## 128 Thyr_AgvsInh_Down GC_AgvsInh_Down 116.7920632 6.364375e-89 63
## 129 Ret_AgvsInh_Up GC_AgvsInh_Down 4.4865051 1.791092e-19 75
## 130 Ret_AgvsInh_Down GC_AgvsInh_Down 0.8402834 7.694561e-01 14
## 131 Estr_AgvsInh_Up GC_AgvsInh_Down 0.0000000 1.000000e+00 0
## 132 Estr_AgvsInh_Down GC_AgvsInh_Down 75.8000556 4.816229e-17 12
## 133 Andr_AgvsInh_Up GC_AgvsInh_Down 65.5910019 7.080601e-105 90
## 134 Andr_AgvsInh_Down GC_AgvsInh_Down 1.9048813 1.328217e-01 5
## 135 GC_AgvsInh_Up GC_AgvsInh_Down 0.0000000 1.000000e+00 0
## 136 GC_AgvsInh_Down GC_AgvsInh_Down Inf 0.000000e+00 171
## 137 LivX_AgvsInh_Up GC_AgvsInh_Down 0.0000000 1.000000e+00 0
## 138 LivX_AgvsInh_Down GC_AgvsInh_Down 405.5958594 1.507718e-194 117
## 139 AhHyd_AgvsInh_Up GC_AgvsInh_Down 39.3284554 1.460928e-34 31
## 140 AhHyd_AgvsInh_Down GC_AgvsInh_Down 3.1888304 1.997478e-03 10
## 141 Thyr_AgvsInh_Up LivX_AgvsInh_Up 33.4636059 6.733621e-66 67
## 142 Thyr_AgvsInh_Down LivX_AgvsInh_Up 0.3626601 9.358337e-01 1
## 143 Ret_AgvsInh_Up LivX_AgvsInh_Up 0.6135011 9.966646e-01 29
## 144 Ret_AgvsInh_Down LivX_AgvsInh_Up 8.1934729 1.435075e-55 129
## 145 Estr_AgvsInh_Up LivX_AgvsInh_Up 26.1449143 1.805373e-11 11
## 146 Estr_AgvsInh_Down LivX_AgvsInh_Up 4.0332363 9.741783e-02 2
## 147 Andr_AgvsInh_Up LivX_AgvsInh_Up 0.1456846 9.988374e-01 1
## 148 Andr_AgvsInh_Down LivX_AgvsInh_Up 15.9099839 1.038155e-36 49
## 149 GC_AgvsInh_Up LivX_AgvsInh_Up 168.1952201 1.198721e-264 198
## 150 GC_AgvsInh_Down LivX_AgvsInh_Up 0.0000000 1.000000e+00 0
## 151 LivX_AgvsInh_Up LivX_AgvsInh_Up Inf 0.000000e+00 291
## 152 LivX_AgvsInh_Down LivX_AgvsInh_Up 0.0000000 1.000000e+00 0
## 153 AhHyd_AgvsInh_Up LivX_AgvsInh_Up 3.8549883 1.817733e-03 8
## 154 AhHyd_AgvsInh_Down LivX_AgvsInh_Up 4.1298212 2.855977e-07 21
## 155 Thyr_AgvsInh_Up LivX_AgvsInh_Down 0.3836762 9.256038e-01 1
## 156 Thyr_AgvsInh_Down LivX_AgvsInh_Down 87.1889226 3.444565e-79 60
## 157 Ret_AgvsInh_Up LivX_AgvsInh_Down 6.7392307 1.135165e-35 103
## 158 Ret_AgvsInh_Down LivX_AgvsInh_Down 0.6261832 9.622804e-01 12
## 159 Estr_AgvsInh_Up LivX_AgvsInh_Down 0.0000000 1.000000e+00 0
## 160 Estr_AgvsInh_Down LivX_AgvsInh_Down 92.0962413 3.200680e-20 14
## 161 Andr_AgvsInh_Up LivX_AgvsInh_Down 40.3770388 3.577890e-82 80
## 162 Andr_AgvsInh_Down LivX_AgvsInh_Down 3.9464174 2.313084e-04 11
## 163 GC_AgvsInh_Up LivX_AgvsInh_Down 0.0000000 1.000000e+00 0
## 164 GC_AgvsInh_Down LivX_AgvsInh_Down 405.5958594 1.507718e-194 117
## 165 LivX_AgvsInh_Up LivX_AgvsInh_Down 0.0000000 1.000000e+00 0
## 166 LivX_AgvsInh_Down LivX_AgvsInh_Down Inf 0.000000e+00 192
## 167 AhHyd_AgvsInh_Up LivX_AgvsInh_Down 30.7704613 7.100713e-30 29
## 168 AhHyd_AgvsInh_Down LivX_AgvsInh_Down 5.1142504 2.302002e-07 17
## 169 Thyr_AgvsInh_Up AhHyd_AgvsInh_Up 6.0033903 1.118496e-04 8
## 170 Thyr_AgvsInh_Down AhHyd_AgvsInh_Up 23.9241607 8.043640e-18 18
## 171 Ret_AgvsInh_Up AhHyd_AgvsInh_Up 3.3653543 1.043005e-08 41
## 172 Ret_AgvsInh_Down AhHyd_AgvsInh_Up 1.8583830 1.660658e-02 18
## 173 Estr_AgvsInh_Up AhHyd_AgvsInh_Up 13.6903593 1.865553e-03 3
## 174 Estr_AgvsInh_Down AhHyd_AgvsInh_Up 17.2593505 1.011205e-03 3
## 175 Andr_AgvsInh_Up AhHyd_AgvsInh_Up 32.9806140 7.366421e-44 44
## 176 Andr_AgvsInh_Down AhHyd_AgvsInh_Up 0.0000000 1.000000e+00 0
## 177 GC_AgvsInh_Up AhHyd_AgvsInh_Up 3.3853489 2.319710e-03 9
## 178 GC_AgvsInh_Down AhHyd_AgvsInh_Up 39.3284554 1.460928e-34 31
## 179 LivX_AgvsInh_Up AhHyd_AgvsInh_Up 3.8549883 1.817733e-03 8
## 180 LivX_AgvsInh_Down AhHyd_AgvsInh_Up 30.7704613 7.100713e-30 29
## 181 AhHyd_AgvsInh_Up AhHyd_AgvsInh_Up Inf 1.904254e-279 110
## 182 AhHyd_AgvsInh_Down AhHyd_AgvsInh_Up 0.0000000 1.000000e+00 0
## 183 Thyr_AgvsInh_Up AhHyd_AgvsInh_Down 3.1448076 1.367533e-03 11
## 184 Thyr_AgvsInh_Down AhHyd_AgvsInh_Down 1.5610879 2.634182e-01 4
## 185 Ret_AgvsInh_Up AhHyd_AgvsInh_Down 9.5782571 1.681532e-71 172
## 186 Ret_AgvsInh_Down AhHyd_AgvsInh_Down 1.1795080 2.214766e-01 31
## 187 Estr_AgvsInh_Up AhHyd_AgvsInh_Down 1.6179044 4.691410e-01 1
## 188 Estr_AgvsInh_Down AhHyd_AgvsInh_Down 4.1955388 9.126644e-02 2
## 189 Andr_AgvsInh_Up AhHyd_AgvsInh_Down 0.0000000 1.000000e+00 0
## 190 Andr_AgvsInh_Down AhHyd_AgvsInh_Down 22.2812178 1.946507e-50 59
## 191 GC_AgvsInh_Up AhHyd_AgvsInh_Down 4.0341595 2.103207e-08 26
## 192 GC_AgvsInh_Down AhHyd_AgvsInh_Down 3.1888304 1.997478e-03 10
## 193 LivX_AgvsInh_Up AhHyd_AgvsInh_Down 4.1298212 2.855977e-07 21
## 194 LivX_AgvsInh_Down AhHyd_AgvsInh_Down 5.1142504 2.302002e-07 17
## 195 AhHyd_AgvsInh_Up AhHyd_AgvsInh_Down 0.0000000 1.000000e+00 0
## 196 AhHyd_AgvsInh_Down AhHyd_AgvsInh_Down Inf 0.000000e+00 280
<- Res
ResMod
$DEGs == ResMod$KBase, ]$OR <- 1
ResMod[ResMod$DEGs == ResMod$KBase, ]$Pval <- 1
ResMod[ResMod
ResMod## DEGs KBase OR Pval Numbers
## 1 Thyr_AgvsInh_Up Thyr_AgvsInh_Up 1.0000000 1.000000e+00 191
## 2 Thyr_AgvsInh_Down Thyr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 3 Ret_AgvsInh_Up Thyr_AgvsInh_Up 4.0530055 1.421630e-18 79
## 4 Ret_AgvsInh_Down Thyr_AgvsInh_Up 2.9744832 8.726946e-09 45
## 5 Estr_AgvsInh_Up Thyr_AgvsInh_Up 25.6461692 6.974103e-09 8
## 6 Estr_AgvsInh_Down Thyr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 7 Andr_AgvsInh_Up Thyr_AgvsInh_Up 0.9191247 6.342118e-01 4
## 8 Andr_AgvsInh_Down Thyr_AgvsInh_Up 11.5631303 2.322727e-18 27
## 9 GC_AgvsInh_Up Thyr_AgvsInh_Up 38.4467168 6.298575e-85 85
## 10 GC_AgvsInh_Down Thyr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 11 LivX_AgvsInh_Up Thyr_AgvsInh_Up 33.4636059 6.733621e-66 67
## 12 LivX_AgvsInh_Down Thyr_AgvsInh_Up 0.3836762 9.256038e-01 1
## 13 AhHyd_AgvsInh_Up Thyr_AgvsInh_Up 6.0033903 1.118496e-04 8
## 14 AhHyd_AgvsInh_Down Thyr_AgvsInh_Up 3.1448076 1.367533e-03 11
## 15 Thyr_AgvsInh_Up Thyr_AgvsInh_Down 0.0000000 1.000000e+00 0
## 16 Thyr_AgvsInh_Down Thyr_AgvsInh_Down 1.0000000 1.000000e+00 133
## 17 Ret_AgvsInh_Up Thyr_AgvsInh_Down 2.0123753 5.901433e-04 35
## 18 Ret_AgvsInh_Down Thyr_AgvsInh_Down 2.0979815 1.731715e-03 24
## 19 Estr_AgvsInh_Up Thyr_AgvsInh_Down 3.4551786 2.586155e-01 1
## 20 Estr_AgvsInh_Down Thyr_AgvsInh_Down 117.3982815 1.999327e-20 13
## 21 Andr_AgvsInh_Up Thyr_AgvsInh_Down 76.9388578 1.019081e-93 77
## 22 Andr_AgvsInh_Down Thyr_AgvsInh_Down 1.4500290 3.484756e-01 3
## 23 GC_AgvsInh_Up Thyr_AgvsInh_Down 0.0000000 1.000000e+00 0
## 24 GC_AgvsInh_Down Thyr_AgvsInh_Down 116.7920632 6.364375e-89 63
## 25 LivX_AgvsInh_Up Thyr_AgvsInh_Down 0.3626601 9.358337e-01 1
## 26 LivX_AgvsInh_Down Thyr_AgvsInh_Down 87.1889226 3.444565e-79 60
## 27 AhHyd_AgvsInh_Up Thyr_AgvsInh_Down 23.9241607 8.043640e-18 18
## 28 AhHyd_AgvsInh_Down Thyr_AgvsInh_Down 1.5610879 2.634182e-01 4
## 29 Thyr_AgvsInh_Up Ret_AgvsInh_Up 4.0530055 1.421630e-18 79
## 30 Thyr_AgvsInh_Down Ret_AgvsInh_Up 2.0123753 5.901433e-04 35
## 31 Ret_AgvsInh_Up Ret_AgvsInh_Up 1.0000000 1.000000e+00 2171
## 32 Ret_AgvsInh_Down Ret_AgvsInh_Up 0.0000000 1.000000e+00 0
## 33 Estr_AgvsInh_Up Ret_AgvsInh_Up 2.9371490 5.653845e-03 11
## 34 Estr_AgvsInh_Down Ret_AgvsInh_Up 0.7286571 7.778992e-01 3
## 35 Andr_AgvsInh_Up Ret_AgvsInh_Up 2.4419925 8.941044e-12 97
## 36 Andr_AgvsInh_Down Ret_AgvsInh_Up 1.4457123 1.956813e-02 46
## 37 GC_AgvsInh_Up Ret_AgvsInh_Up 0.4640398 9.999957e-01 29
## 38 GC_AgvsInh_Down Ret_AgvsInh_Up 4.4865051 1.791092e-19 75
## 39 LivX_AgvsInh_Up Ret_AgvsInh_Up 0.6135011 9.966646e-01 29
## 40 LivX_AgvsInh_Down Ret_AgvsInh_Up 6.7392307 1.135165e-35 103
## 41 AhHyd_AgvsInh_Up Ret_AgvsInh_Up 3.3653543 1.043005e-08 41
## 42 AhHyd_AgvsInh_Down Ret_AgvsInh_Up 9.5782571 1.681532e-71 172
## 43 Thyr_AgvsInh_Up Ret_AgvsInh_Down 2.9744832 8.726946e-09 45
## 44 Thyr_AgvsInh_Down Ret_AgvsInh_Down 2.0979815 1.731715e-03 24
## 45 Ret_AgvsInh_Up Ret_AgvsInh_Down 0.0000000 1.000000e+00 0
## 46 Ret_AgvsInh_Down Ret_AgvsInh_Down 1.0000000 1.000000e+00 1370
## 47 Estr_AgvsInh_Up Ret_AgvsInh_Down 4.9765736 1.154895e-04 11
## 48 Estr_AgvsInh_Down Ret_AgvsInh_Down 1.7186678 2.343454e-01 4
## 49 Andr_AgvsInh_Up Ret_AgvsInh_Down 0.5476547 9.972662e-01 18
## 50 Andr_AgvsInh_Down Ret_AgvsInh_Down 6.5365413 9.213323e-34 89
## 51 GC_AgvsInh_Up Ret_AgvsInh_Down 8.5752537 5.706244e-73 167
## 52 GC_AgvsInh_Down Ret_AgvsInh_Down 0.8402834 7.694561e-01 14
## 53 LivX_AgvsInh_Up Ret_AgvsInh_Down 8.1934729 1.435075e-55 129
## 54 LivX_AgvsInh_Down Ret_AgvsInh_Down 0.6261832 9.622804e-01 12
## 55 AhHyd_AgvsInh_Up Ret_AgvsInh_Down 1.8583830 1.660658e-02 18
## 56 AhHyd_AgvsInh_Down Ret_AgvsInh_Down 1.1795080 2.214766e-01 31
## 57 Thyr_AgvsInh_Up Estr_AgvsInh_Up 25.6461692 6.974103e-09 8
## 58 Thyr_AgvsInh_Down Estr_AgvsInh_Up 3.4551786 2.586155e-01 1
## 59 Ret_AgvsInh_Up Estr_AgvsInh_Up 2.9371490 5.653845e-03 11
## 60 Ret_AgvsInh_Down Estr_AgvsInh_Up 4.9765736 1.154895e-04 11
## 61 Estr_AgvsInh_Up Estr_AgvsInh_Up 1.0000000 1.000000e+00 32
## 62 Estr_AgvsInh_Down Estr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 63 Andr_AgvsInh_Up Estr_AgvsInh_Up 6.2071211 5.693650e-03 4
## 64 Andr_AgvsInh_Down Estr_AgvsInh_Up 4.1995573 8.982384e-02 2
## 65 GC_AgvsInh_Up Estr_AgvsInh_Up 50.3969154 6.985781e-21 18
## 66 GC_AgvsInh_Down Estr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 67 LivX_AgvsInh_Up Estr_AgvsInh_Up 26.1449143 1.805373e-11 11
## 68 LivX_AgvsInh_Down Estr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 69 AhHyd_AgvsInh_Up Estr_AgvsInh_Up 13.6903593 1.865553e-03 3
## 70 AhHyd_AgvsInh_Down Estr_AgvsInh_Up 1.6179044 4.691410e-01 1
## 71 Thyr_AgvsInh_Up Estr_AgvsInh_Down 0.0000000 1.000000e+00 0
## 72 Thyr_AgvsInh_Down Estr_AgvsInh_Down 117.3982815 1.999327e-20 13
## 73 Ret_AgvsInh_Up Estr_AgvsInh_Down 0.7286571 7.778992e-01 3
## 74 Ret_AgvsInh_Down Estr_AgvsInh_Down 1.7186678 2.343454e-01 4
## 75 Estr_AgvsInh_Up Estr_AgvsInh_Down 0.0000000 1.000000e+00 0
## 76 Estr_AgvsInh_Down Estr_AgvsInh_Down 1.0000000 1.000000e+00 26
## 77 Andr_AgvsInh_Up Estr_AgvsInh_Down 32.5542122 4.010907e-12 11
## 78 Andr_AgvsInh_Down Estr_AgvsInh_Down 8.2554654 7.644201e-03 3
## 79 GC_AgvsInh_Up Estr_AgvsInh_Down 4.9025775 2.933257e-02 3
## 80 GC_AgvsInh_Down Estr_AgvsInh_Down 75.8000556 4.816229e-17 12
## 81 LivX_AgvsInh_Up Estr_AgvsInh_Down 4.0332363 9.741783e-02 2
## 82 LivX_AgvsInh_Down Estr_AgvsInh_Down 92.0962413 3.200680e-20 14
## 83 AhHyd_AgvsInh_Up Estr_AgvsInh_Down 17.2593505 1.011205e-03 3
## 84 AhHyd_AgvsInh_Down Estr_AgvsInh_Down 4.1955388 9.126644e-02 2
## 85 Thyr_AgvsInh_Up Andr_AgvsInh_Up 0.9191247 6.342118e-01 4
## 86 Thyr_AgvsInh_Down Andr_AgvsInh_Up 76.9388578 1.019081e-93 77
## 87 Ret_AgvsInh_Up Andr_AgvsInh_Up 2.4419925 8.941044e-12 97
## 88 Ret_AgvsInh_Down Andr_AgvsInh_Up 0.5476547 9.972662e-01 18
## 89 Estr_AgvsInh_Up Andr_AgvsInh_Up 6.2071211 5.693650e-03 4
## 90 Estr_AgvsInh_Down Andr_AgvsInh_Up 32.5542122 4.010907e-12 11
## 91 Andr_AgvsInh_Up Andr_AgvsInh_Up 1.0000000 1.000000e+00 325
## 92 Andr_AgvsInh_Down Andr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 93 GC_AgvsInh_Up Andr_AgvsInh_Up 0.4596587 9.721261e-01 4
## 94 GC_AgvsInh_Down Andr_AgvsInh_Up 65.5910019 7.080601e-105 90
## 95 LivX_AgvsInh_Up Andr_AgvsInh_Up 0.1456846 9.988374e-01 1
## 96 LivX_AgvsInh_Down Andr_AgvsInh_Up 40.3770388 3.577890e-82 80
## 97 AhHyd_AgvsInh_Up Andr_AgvsInh_Up 32.9806140 7.366421e-44 44
## 98 AhHyd_AgvsInh_Down Andr_AgvsInh_Up 0.0000000 1.000000e+00 0
## 99 Thyr_AgvsInh_Up Andr_AgvsInh_Down 11.5631303 2.322727e-18 27
## 100 Thyr_AgvsInh_Down Andr_AgvsInh_Down 1.4500290 3.484756e-01 3
## 101 Ret_AgvsInh_Up Andr_AgvsInh_Down 1.4457123 1.956813e-02 46
## 102 Ret_AgvsInh_Down Andr_AgvsInh_Down 6.5365413 9.213323e-34 89
## 103 Estr_AgvsInh_Up Andr_AgvsInh_Down 4.1995573 8.982384e-02 2
## 104 Estr_AgvsInh_Down Andr_AgvsInh_Down 8.2554654 7.644201e-03 3
## 105 Andr_AgvsInh_Up Andr_AgvsInh_Down 0.0000000 1.000000e+00 0
## 106 Andr_AgvsInh_Down Andr_AgvsInh_Down 1.0000000 1.000000e+00 225
## 107 GC_AgvsInh_Up Andr_AgvsInh_Down 18.6084381 1.917203e-51 66
## 108 GC_AgvsInh_Down Andr_AgvsInh_Down 1.9048813 1.328217e-01 5
## 109 LivX_AgvsInh_Up Andr_AgvsInh_Down 15.9099839 1.038155e-36 49
## 110 LivX_AgvsInh_Down Andr_AgvsInh_Down 3.9464174 2.313084e-04 11
## 111 AhHyd_AgvsInh_Up Andr_AgvsInh_Down 0.0000000 1.000000e+00 0
## 112 AhHyd_AgvsInh_Down Andr_AgvsInh_Down 22.2812178 1.946507e-50 59
## 113 Thyr_AgvsInh_Up GC_AgvsInh_Up 38.4467168 6.298575e-85 85
## 114 Thyr_AgvsInh_Down GC_AgvsInh_Up 0.0000000 1.000000e+00 0
## 115 Ret_AgvsInh_Up GC_AgvsInh_Up 0.4640398 9.999957e-01 29
## 116 Ret_AgvsInh_Down GC_AgvsInh_Up 8.5752537 5.706244e-73 167
## 117 Estr_AgvsInh_Up GC_AgvsInh_Up 50.3969154 6.985781e-21 18
## 118 Estr_AgvsInh_Down GC_AgvsInh_Up 4.9025775 2.933257e-02 3
## 119 Andr_AgvsInh_Up GC_AgvsInh_Up 0.4596587 9.721261e-01 4
## 120 Andr_AgvsInh_Down GC_AgvsInh_Up 18.6084381 1.917203e-51 66
## 121 GC_AgvsInh_Up GC_AgvsInh_Up 1.0000000 1.000000e+00 373
## 122 GC_AgvsInh_Down GC_AgvsInh_Up 0.0000000 1.000000e+00 0
## 123 LivX_AgvsInh_Up GC_AgvsInh_Up 168.1952201 1.198721e-264 198
## 124 LivX_AgvsInh_Down GC_AgvsInh_Up 0.0000000 1.000000e+00 0
## 125 AhHyd_AgvsInh_Up GC_AgvsInh_Up 3.3853489 2.319710e-03 9
## 126 AhHyd_AgvsInh_Down GC_AgvsInh_Up 4.0341595 2.103207e-08 26
## 127 Thyr_AgvsInh_Up GC_AgvsInh_Down 0.0000000 1.000000e+00 0
## 128 Thyr_AgvsInh_Down GC_AgvsInh_Down 116.7920632 6.364375e-89 63
## 129 Ret_AgvsInh_Up GC_AgvsInh_Down 4.4865051 1.791092e-19 75
## 130 Ret_AgvsInh_Down GC_AgvsInh_Down 0.8402834 7.694561e-01 14
## 131 Estr_AgvsInh_Up GC_AgvsInh_Down 0.0000000 1.000000e+00 0
## 132 Estr_AgvsInh_Down GC_AgvsInh_Down 75.8000556 4.816229e-17 12
## 133 Andr_AgvsInh_Up GC_AgvsInh_Down 65.5910019 7.080601e-105 90
## 134 Andr_AgvsInh_Down GC_AgvsInh_Down 1.9048813 1.328217e-01 5
## 135 GC_AgvsInh_Up GC_AgvsInh_Down 0.0000000 1.000000e+00 0
## 136 GC_AgvsInh_Down GC_AgvsInh_Down 1.0000000 1.000000e+00 171
## 137 LivX_AgvsInh_Up GC_AgvsInh_Down 0.0000000 1.000000e+00 0
## 138 LivX_AgvsInh_Down GC_AgvsInh_Down 405.5958594 1.507718e-194 117
## 139 AhHyd_AgvsInh_Up GC_AgvsInh_Down 39.3284554 1.460928e-34 31
## 140 AhHyd_AgvsInh_Down GC_AgvsInh_Down 3.1888304 1.997478e-03 10
## 141 Thyr_AgvsInh_Up LivX_AgvsInh_Up 33.4636059 6.733621e-66 67
## 142 Thyr_AgvsInh_Down LivX_AgvsInh_Up 0.3626601 9.358337e-01 1
## 143 Ret_AgvsInh_Up LivX_AgvsInh_Up 0.6135011 9.966646e-01 29
## 144 Ret_AgvsInh_Down LivX_AgvsInh_Up 8.1934729 1.435075e-55 129
## 145 Estr_AgvsInh_Up LivX_AgvsInh_Up 26.1449143 1.805373e-11 11
## 146 Estr_AgvsInh_Down LivX_AgvsInh_Up 4.0332363 9.741783e-02 2
## 147 Andr_AgvsInh_Up LivX_AgvsInh_Up 0.1456846 9.988374e-01 1
## 148 Andr_AgvsInh_Down LivX_AgvsInh_Up 15.9099839 1.038155e-36 49
## 149 GC_AgvsInh_Up LivX_AgvsInh_Up 168.1952201 1.198721e-264 198
## 150 GC_AgvsInh_Down LivX_AgvsInh_Up 0.0000000 1.000000e+00 0
## 151 LivX_AgvsInh_Up LivX_AgvsInh_Up 1.0000000 1.000000e+00 291
## 152 LivX_AgvsInh_Down LivX_AgvsInh_Up 0.0000000 1.000000e+00 0
## 153 AhHyd_AgvsInh_Up LivX_AgvsInh_Up 3.8549883 1.817733e-03 8
## 154 AhHyd_AgvsInh_Down LivX_AgvsInh_Up 4.1298212 2.855977e-07 21
## 155 Thyr_AgvsInh_Up LivX_AgvsInh_Down 0.3836762 9.256038e-01 1
## 156 Thyr_AgvsInh_Down LivX_AgvsInh_Down 87.1889226 3.444565e-79 60
## 157 Ret_AgvsInh_Up LivX_AgvsInh_Down 6.7392307 1.135165e-35 103
## 158 Ret_AgvsInh_Down LivX_AgvsInh_Down 0.6261832 9.622804e-01 12
## 159 Estr_AgvsInh_Up LivX_AgvsInh_Down 0.0000000 1.000000e+00 0
## 160 Estr_AgvsInh_Down LivX_AgvsInh_Down 92.0962413 3.200680e-20 14
## 161 Andr_AgvsInh_Up LivX_AgvsInh_Down 40.3770388 3.577890e-82 80
## 162 Andr_AgvsInh_Down LivX_AgvsInh_Down 3.9464174 2.313084e-04 11
## 163 GC_AgvsInh_Up LivX_AgvsInh_Down 0.0000000 1.000000e+00 0
## 164 GC_AgvsInh_Down LivX_AgvsInh_Down 405.5958594 1.507718e-194 117
## 165 LivX_AgvsInh_Up LivX_AgvsInh_Down 0.0000000 1.000000e+00 0
## 166 LivX_AgvsInh_Down LivX_AgvsInh_Down 1.0000000 1.000000e+00 192
## 167 AhHyd_AgvsInh_Up LivX_AgvsInh_Down 30.7704613 7.100713e-30 29
## 168 AhHyd_AgvsInh_Down LivX_AgvsInh_Down 5.1142504 2.302002e-07 17
## 169 Thyr_AgvsInh_Up AhHyd_AgvsInh_Up 6.0033903 1.118496e-04 8
## 170 Thyr_AgvsInh_Down AhHyd_AgvsInh_Up 23.9241607 8.043640e-18 18
## 171 Ret_AgvsInh_Up AhHyd_AgvsInh_Up 3.3653543 1.043005e-08 41
## 172 Ret_AgvsInh_Down AhHyd_AgvsInh_Up 1.8583830 1.660658e-02 18
## 173 Estr_AgvsInh_Up AhHyd_AgvsInh_Up 13.6903593 1.865553e-03 3
## 174 Estr_AgvsInh_Down AhHyd_AgvsInh_Up 17.2593505 1.011205e-03 3
## 175 Andr_AgvsInh_Up AhHyd_AgvsInh_Up 32.9806140 7.366421e-44 44
## 176 Andr_AgvsInh_Down AhHyd_AgvsInh_Up 0.0000000 1.000000e+00 0
## 177 GC_AgvsInh_Up AhHyd_AgvsInh_Up 3.3853489 2.319710e-03 9
## 178 GC_AgvsInh_Down AhHyd_AgvsInh_Up 39.3284554 1.460928e-34 31
## 179 LivX_AgvsInh_Up AhHyd_AgvsInh_Up 3.8549883 1.817733e-03 8
## 180 LivX_AgvsInh_Down AhHyd_AgvsInh_Up 30.7704613 7.100713e-30 29
## 181 AhHyd_AgvsInh_Up AhHyd_AgvsInh_Up 1.0000000 1.000000e+00 110
## 182 AhHyd_AgvsInh_Down AhHyd_AgvsInh_Up 0.0000000 1.000000e+00 0
## 183 Thyr_AgvsInh_Up AhHyd_AgvsInh_Down 3.1448076 1.367533e-03 11
## 184 Thyr_AgvsInh_Down AhHyd_AgvsInh_Down 1.5610879 2.634182e-01 4
## 185 Ret_AgvsInh_Up AhHyd_AgvsInh_Down 9.5782571 1.681532e-71 172
## 186 Ret_AgvsInh_Down AhHyd_AgvsInh_Down 1.1795080 2.214766e-01 31
## 187 Estr_AgvsInh_Up AhHyd_AgvsInh_Down 1.6179044 4.691410e-01 1
## 188 Estr_AgvsInh_Down AhHyd_AgvsInh_Down 4.1955388 9.126644e-02 2
## 189 Andr_AgvsInh_Up AhHyd_AgvsInh_Down 0.0000000 1.000000e+00 0
## 190 Andr_AgvsInh_Down AhHyd_AgvsInh_Down 22.2812178 1.946507e-50 59
## 191 GC_AgvsInh_Up AhHyd_AgvsInh_Down 4.0341595 2.103207e-08 26
## 192 GC_AgvsInh_Down AhHyd_AgvsInh_Down 3.1888304 1.997478e-03 10
## 193 LivX_AgvsInh_Up AhHyd_AgvsInh_Down 4.1298212 2.855977e-07 21
## 194 LivX_AgvsInh_Down AhHyd_AgvsInh_Down 5.1142504 2.302002e-07 17
## 195 AhHyd_AgvsInh_Up AhHyd_AgvsInh_Down 0.0000000 1.000000e+00 0
## 196 AhHyd_AgvsInh_Down AhHyd_AgvsInh_Down 1.0000000 1.000000e+00 280
DotPlot: visualization I select as significant overlaps having an OR > 2 and at least 25 overlapping genes. Dots are shown for PVals < 0.01 (set in the plot). Max value in the plot must be set according to minimum PVal to avoid dots not to be shown.
<- dplyr::filter(ResMod, OR > 2) %>% dplyr::filter(Numbers > 25)
ResSel min(ResSel$Pval)
## [1] 1.198721e-264
max(ResSel$OR)
## [1] 405.5959
<- ggplot(ResSel, aes(DEGs, KBase, label=Numbers)) +
Dot geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1)) +
ggtitle('Overlap across AgvsInh-modulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_AgvsInh.pdf'), width=8, height=8)
<- c('Thyr_AgvsInh_Up', 'Thyr_AgvsInh_Down', 'Ret_AgvsInh_Up', 'Ret_AgvsInh_Down',
Path 'Estr_AgvsInh_Up', 'Estr_AgvsInh_Down', 'LivX_AgvsInh_Up', 'LivX_AgvsInh_Down')
<- ResSel[ResSel$DEGs %in% Path & ResSel$KBase %in% Path, ]
ResPath
ResPath## DEGs KBase OR Pval Numbers
## 1 Ret_AgvsInh_Up Thyr_AgvsInh_Up 4.053005 1.421630e-18 79
## 2 Ret_AgvsInh_Down Thyr_AgvsInh_Up 2.974483 8.726946e-09 45
## 5 LivX_AgvsInh_Up Thyr_AgvsInh_Up 33.463606 6.733621e-66 67
## 6 Ret_AgvsInh_Up Thyr_AgvsInh_Down 2.012375 5.901433e-04 35
## 9 LivX_AgvsInh_Down Thyr_AgvsInh_Down 87.188923 3.444565e-79 60
## 10 Thyr_AgvsInh_Up Ret_AgvsInh_Up 4.053005 1.421630e-18 79
## 11 Thyr_AgvsInh_Down Ret_AgvsInh_Up 2.012375 5.901433e-04 35
## 14 LivX_AgvsInh_Down Ret_AgvsInh_Up 6.739231 1.135165e-35 103
## 17 Thyr_AgvsInh_Up Ret_AgvsInh_Down 2.974483 8.726946e-09 45
## 20 LivX_AgvsInh_Up Ret_AgvsInh_Down 8.193473 1.435075e-55 129
## 41 Thyr_AgvsInh_Up LivX_AgvsInh_Up 33.463606 6.733621e-66 67
## 42 Ret_AgvsInh_Down LivX_AgvsInh_Up 8.193473 1.435075e-55 129
## 45 Thyr_AgvsInh_Down LivX_AgvsInh_Down 87.188923 3.444565e-79 60
## 46 Ret_AgvsInh_Up LivX_AgvsInh_Down 6.739231 1.135165e-35 103
<- dplyr::filter(ResPath, OR > 2) %>% dplyr::filter(Numbers > 25)
ResPath min(ResPath$Pval)
## [1] 3.444565e-79
max(ResPath$OR)
## [1] 87.18892
<- ggplot(ResPath, aes(DEGs, KBase, label=Numbers)) +
Dot geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1))+
ggtitle('Overlap across AgvsInh-modulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_AgvsInh_Selected.pdf'), width=8, height=8)
<- sessionInfo()
SessionInfo <- date() Date
Date## [1] "Mon Jul 21 23:20:53 2025"
SessionInfo## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] DESeq2_1.38.3 SummarizedExperiment_1.28.0
## [3] Biobase_2.58.0 MatrixGenerics_1.10.0
## [5] matrixStats_0.63.0 GenomicRanges_1.50.2
## [7] GenomeInfoDb_1.34.9 IRanges_2.32.0
## [9] S4Vectors_0.36.1 BiocGenerics_0.44.0
## [11] GeneOverlap_1.34.0 ggplot2_3.4.1
## [13] dplyr_1.1.0 tidyr_1.3.0
##
## loaded via a namespace (and not attached):
## [1] viridis_0.6.2 httr_1.4.5 sass_0.4.5
## [4] viridisLite_0.4.1 bit64_4.0.5 jsonlite_1.8.4
## [7] gtools_3.9.4 bslib_0.4.2 highr_0.10
## [10] blob_1.2.3 GenomeInfoDbData_1.2.9 yaml_2.3.7
## [13] pillar_1.8.1 RSQLite_2.3.0 lattice_0.20-45
## [16] glue_1.6.2 digest_0.6.31 RColorBrewer_1.1-3
## [19] XVector_0.38.0 colorspace_2.1-0 htmltools_0.5.4
## [22] Matrix_1.5-3 XML_3.99-0.13 pkgconfig_2.0.3
## [25] zlibbioc_1.44.0 purrr_1.0.1 xtable_1.8-4
## [28] scales_1.2.1 BiocParallel_1.32.5 tibble_3.2.1
## [31] annotate_1.76.0 KEGGREST_1.38.0 farver_2.1.1
## [34] generics_0.1.3 cachem_1.0.7 withr_2.5.0
## [37] cli_3.6.1 crayon_1.5.2 magrittr_2.0.3
## [40] memoise_2.0.1 evaluate_0.20 fansi_1.0.4
## [43] gplots_3.1.3 textshaping_0.3.6 tools_4.2.1
## [46] lifecycle_1.0.3 locfit_1.5-9.7 munsell_0.5.0
## [49] DelayedArray_0.24.0 Biostrings_2.66.0 AnnotationDbi_1.60.0
## [52] compiler_4.2.1 jquerylib_0.1.4 systemfonts_1.0.4
## [55] caTools_1.18.2 rlang_1.1.1 grid_4.2.1
## [58] RCurl_1.98-1.10 rstudioapi_0.14 labeling_0.4.2
## [61] bitops_1.0-7 rmarkdown_2.20 gtable_0.3.1
## [64] codetools_0.2-19 DBI_1.1.3 R6_2.5.1
## [67] gridExtra_2.3 knitr_1.42 fastmap_1.1.1
## [70] bit_4.0.5 utf8_1.2.3 ragg_1.2.3
## [73] KernSmooth_2.23-20 parallel_4.2.1 Rcpp_1.0.10
## [76] png_0.1-8 vctrs_0.6.2 geneplotter_1.76.0
## [79] tidyselect_1.2.0 xfun_0.37