Functional enrichment analysis with TopGO of WGCNA modules from scRNAseq

1. Environment Set Up

1.1 Values of RMarkdown parameters

for (i in 1:length(params))
  print(paste('Parameter:', names(params)[i], ' - Value:', params[[i]], '- Class:', class(params[[i]])))
## [1] "Parameter: OutputFolder  - Value:  - Class: character"

library(dplyr)
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
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library(ggplot2)
library(gridExtra)
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## Attaching package: 'gridExtra'
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library(viridis)
## Loading required package: viridisLite
library(SummarizedExperiment)
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## Loading required package: matrixStats
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##     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
##     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
##     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
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##     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
##     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
##     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
##     rowWeightedSds, rowWeightedVars
## Loading required package: GenomicRanges
## Loading required package: stats4
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## Attaching package: 'BiocGenerics'
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##     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
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## Loading required package: GenomeInfoDb
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## Welcome to Bioconductor
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library(AnnotationDbi)
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## Attaching package: 'AnnotationDbi'
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library(org.Hs.eg.db)
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library(topGO)
## Loading required package: graph
## Loading required package: GO.db
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## Loading required package: SparseM
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## Attaching package: 'SparseM'
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## groupGOTerms:    GOBPTerm, GOMFTerm, GOCCTerm environments built.
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## Attaching package: 'topGO'
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OutputFolder <- params$OutputFolder

1.2 Helper functions

source('~/EndPoints/bulkRNASeq/8.WGCNA/CTL04/WGCNAHelper.R')

---

2. Data Upload

# List of paths and corresponding names
paths <- list(
  EDCs_Neurons = "/group/testa/Users/davide.castaldi/ENDPOINTS_sc/EDCs_substudy/EDCs_substudy_Neurons_DifferentialModulesGenes/topGoPlot/",
  EDCs_Progenitors = "/group/testa/Users/davide.castaldi/ENDPOINTS_sc/EDCs_substudy/EDCs_substudy_Progenitors_DifferentialModulesGenes/topGoPlot/",
  hormones_Progenitors = "/group/testa/Users/davide.castaldi/ENDPOINTS_sc/hormones_substudy/hormones_substudy_Progenitors_DifferentialModulesGenes/topGoPlot/",
  hormones_Neurons = "/group/testa/Users/davide.castaldi/ENDPOINTS_sc/hormones_substudy/hormones_substudy_Neurons_DifferentialModulesGenes/topGoPlot/"
)

# Function to build GeneVectors list for a given path
buildGeneVector <- function(dir_path) {
  all_files <- list.files(dir_path, full.names = TRUE)
  
  # Get all unique module names based on background file pattern
  bg_files <- grep("_background.txt$", all_files, value = TRUE)
  modules <- gsub(".*module([^.]+)\\..*", "\\1", bg_files)
  
  result <- list()
  
  for (mod in modules) {
    # Match background and top200 files
    bg_file <- list.files(dir_path, pattern = paste0("module", mod, ".*_background.txt$"), full.names = TRUE)
    top_file <- list.files(dir_path, pattern = paste0("module", mod, ".*_top200Genes.txt$"), full.names = TRUE)
    
    # Skip if either file is missing
    if (length(bg_file) == 0 || length(top_file) == 0) {
      warning(paste("Missing file for module:", mod))
      next
    }
    
    # Read genes
    bg_genes <- readLines(bg_file)
    top_genes <- readLines(top_file)
    
    # Create named vector of 0s and 1s
    gene_vector <- as.integer(bg_genes %in% top_genes)
    names(gene_vector) <- bg_genes
    
    # Convert to factor (0 or 1 levels)
    result[[mod]] <- factor(gene_vector, levels = c(0, 1))
  }
  
  return(result)
}

---

3. Gene Ontology Analysis - hormones progenitor

GeneVectors <- buildGeneVector(paths$hormones_Progenitors) %>% as.vector()
modules <- names(GeneVectors)

3.1 Biological Process

ResBP <- list()

for(i in 1:length(modules)){
  BPann <- topGO::annFUN.org(whichOnto="BP", feasibleGenes=names(GeneVectors[[modules[i]]]), mapping="org.Hs.eg.db", ID="symbol") %>% topGO::inverseList()

  Res <- topGOResults(Genes=GeneVectors[[modules[i]]], gene2GO=BPann, ontology='BP', 
                      description=NULL, nodeSize=15, algorithm='weight01', 
                      statistic='fisher', EnTh=2, PvalTh=0.01, minTerms=12)
  print(paste('Significant BP terms for', modules[i], 'module:', dim(Res$ResSel)[1]))
  ResBP[[i]] <- Res
  names(ResBP)[i] <- modules[i]
  #write.table(Res$ResSel, file=paste0(OutputFolder, modules[i], '_BP.txt'), sep='\t', row.names=FALSE)
}
## 
## Building most specific GOs .....
##  ( 9519 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 13352 GO terms and 30162 relations. )
## 
## Annotating nodes ...............
##  ( 6661 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1511 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 15:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  4 nodes to be scored    (0 eliminated genes)
## 
##   Level 13:  15 nodes to be scored   (56 eliminated genes)
## 
##   Level 12:  36 nodes to be scored   (140 eliminated genes)
## 
##   Level 11:  68 nodes to be scored   (1065 eliminated genes)
## 
##   Level 10:  119 nodes to be scored  (1949 eliminated genes)
## 
##   Level 9:   178 nodes to be scored  (2390 eliminated genes)
## 
##   Level 8:   192 nodes to be scored  (3110 eliminated genes)
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##   Level 7:   237 nodes to be scored  (3983 eliminated genes)
## 
##   Level 6:   253 nodes to be scored  (4964 eliminated genes)
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##   Level 5:   201 nodes to be scored  (5728 eliminated genes)
## 
##   Level 4:   128 nodes to be scored  (6281 eliminated genes)
## 
##   Level 3:   60 nodes to be scored   (6447 eliminated genes)
## 
##   Level 2:   17 nodes to be scored   (6558 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6592 eliminated genes)
## Warning: There was 1 warning in `dplyr::filter()`.
## ℹ In argument: `as.numeric(Statistics) <= PvalTh`.
## Caused by warning:
## ! NAs introduced by coercion
## [1] "Significant BP terms for burlywood module: 90"
## 
## Building most specific GOs .....
##  ( 9519 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 13352 GO terms and 30162 relations. )
## 
## Annotating nodes ...............
##  ( 6661 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 2558 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 17:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 16:  4 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  11 nodes to be scored   (15 eliminated genes)
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##   Level 14:  14 nodes to be scored   (60 eliminated genes)
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##   Level 13:  34 nodes to be scored   (218 eliminated genes)
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##   Level 12:  61 nodes to be scored   (434 eliminated genes)
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##   Level 11:  107 nodes to be scored  (1449 eliminated genes)
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##   Level 10:  213 nodes to be scored  (2264 eliminated genes)
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##   Level 9:   308 nodes to be scored  (2917 eliminated genes)
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##   Level 8:   381 nodes to be scored  (3842 eliminated genes)
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##   Level 7:   445 nodes to be scored  (4820 eliminated genes)
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##   Level 6:   421 nodes to be scored  (5592 eliminated genes)
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##   Level 5:   290 nodes to be scored  (6074 eliminated genes)
## 
##   Level 4:   172 nodes to be scored  (6389 eliminated genes)
## 
##   Level 3:   78 nodes to be scored   (6499 eliminated genes)
## 
##   Level 2:   17 nodes to be scored   (6559 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6595 eliminated genes)
## [1] "Significant BP terms for chocolate module: 39"
## 
## Building most specific GOs .....
##  ( 9519 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 13352 GO terms and 30162 relations. )
## 
## Annotating nodes ...............
##  ( 6661 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 87 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   1 nodes to be scored    (25 eliminated genes)
## 
##   Level 8:   2 nodes to be scored    (66 eliminated genes)
## 
##   Level 7:   7 nodes to be scored    (99 eliminated genes)
## 
##   Level 6:   13 nodes to be scored   (196 eliminated genes)
## 
##   Level 5:   17 nodes to be scored   (1218 eliminated genes)
## 
##   Level 4:   19 nodes to be scored   (2656 eliminated genes)
## 
##   Level 3:   15 nodes to be scored   (4838 eliminated genes)
## 
##   Level 2:   9 nodes to be scored    (6376 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6486 eliminated genes)
## [1] "Significant BP terms for darkgoldenrod module: 12"
## 
## Building most specific GOs .....
##  ( 9519 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 13352 GO terms and 30162 relations. )
## 
## Annotating nodes ...............
##  ( 6661 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 2372 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  9 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  17 nodes to be scored   (18 eliminated genes)
## 
##   Level 13:  33 nodes to be scored   (194 eliminated genes)
## 
##   Level 12:  53 nodes to be scored   (495 eliminated genes)
## 
##   Level 11:  104 nodes to be scored  (1457 eliminated genes)
## 
##   Level 10:  197 nodes to be scored  (2173 eliminated genes)
## 
##   Level 9:   287 nodes to be scored  (2830 eliminated genes)
## 
##   Level 8:   344 nodes to be scored  (3729 eliminated genes)
## 
##   Level 7:   407 nodes to be scored  (4719 eliminated genes)
## 
##   Level 6:   381 nodes to be scored  (5585 eliminated genes)
## 
##   Level 5:   277 nodes to be scored  (6043 eliminated genes)
## 
##   Level 4:   164 nodes to be scored  (6391 eliminated genes)
## 
##   Level 3:   79 nodes to be scored   (6513 eliminated genes)
## 
##   Level 2:   18 nodes to be scored   (6564 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6601 eliminated genes)
## [1] "Significant BP terms for dimgrey module: 23"
## 
## Building most specific GOs .....
##  ( 9519 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 13352 GO terms and 30162 relations. )
## 
## Annotating nodes ...............
##  ( 6661 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 2267 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 17:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 16:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  11 nodes to be scored   (15 eliminated genes)
## 
##   Level 14:  20 nodes to be scored   (48 eliminated genes)
## 
##   Level 13:  33 nodes to be scored   (192 eliminated genes)
## 
##   Level 12:  55 nodes to be scored   (483 eliminated genes)
## 
##   Level 11:  100 nodes to be scored  (1403 eliminated genes)
## 
##   Level 10:  185 nodes to be scored  (2252 eliminated genes)
## 
##   Level 9:   276 nodes to be scored  (2888 eliminated genes)
## 
##   Level 8:   331 nodes to be scored  (3779 eliminated genes)
## 
##   Level 7:   381 nodes to be scored  (4695 eliminated genes)
## 
##   Level 6:   366 nodes to be scored  (5505 eliminated genes)
## 
##   Level 5:   268 nodes to be scored  (6011 eliminated genes)
## 
##   Level 4:   147 nodes to be scored  (6385 eliminated genes)
## 
##   Level 3:   73 nodes to be scored   (6510 eliminated genes)
## 
##   Level 2:   16 nodes to be scored   (6561 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6594 eliminated genes)
## [1] "Significant BP terms for indianred module: 15"
## 
## Building most specific GOs .....
##  ( 9519 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 13352 GO terms and 30162 relations. )
## 
## Annotating nodes ...............
##  ( 6661 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 2050 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 17:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 16:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  4 nodes to be scored    (15 eliminated genes)
## 
##   Level 14:  11 nodes to be scored   (28 eliminated genes)
## 
##   Level 13:  28 nodes to be scored   (81 eliminated genes)
## 
##   Level 12:  50 nodes to be scored   (447 eliminated genes)
## 
##   Level 11:  71 nodes to be scored   (1467 eliminated genes)
## 
##   Level 10:  148 nodes to be scored  (2273 eliminated genes)
## 
##   Level 9:   233 nodes to be scored  (2723 eliminated genes)
## 
##   Level 8:   290 nodes to be scored  (3675 eliminated genes)
## 
##   Level 7:   366 nodes to be scored  (4578 eliminated genes)
## 
##   Level 6:   349 nodes to be scored  (5413 eliminated genes)
## 
##   Level 5:   262 nodes to be scored  (6037 eliminated genes)
## 
##   Level 4:   148 nodes to be scored  (6385 eliminated genes)
## 
##   Level 3:   69 nodes to be scored   (6502 eliminated genes)
## 
##   Level 2:   17 nodes to be scored   (6564 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6596 eliminated genes)
## [1] "Significant BP terms for lemonchiffon module: 36"
## 
## Building most specific GOs .....
##  ( 9519 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 13352 GO terms and 30162 relations. )
## 
## Annotating nodes ...............
##  ( 6661 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 2043 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 17:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 16:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  9 nodes to be scored    (15 eliminated genes)
## 
##   Level 14:  16 nodes to be scored   (59 eliminated genes)
## 
##   Level 13:  32 nodes to be scored   (188 eliminated genes)
## 
##   Level 12:  43 nodes to be scored   (462 eliminated genes)
## 
##   Level 11:  92 nodes to be scored   (1423 eliminated genes)
## 
##   Level 10:  154 nodes to be scored  (2170 eliminated genes)
## 
##   Level 9:   241 nodes to be scored  (2689 eliminated genes)
## 
##   Level 8:   281 nodes to be scored  (3556 eliminated genes)
## 
##   Level 7:   352 nodes to be scored  (4570 eliminated genes)
## 
##   Level 6:   338 nodes to be scored  (5474 eliminated genes)
## 
##   Level 5:   256 nodes to be scored  (6074 eliminated genes)
## 
##   Level 4:   137 nodes to be scored  (6368 eliminated genes)
## 
##   Level 3:   70 nodes to be scored   (6503 eliminated genes)
## 
##   Level 2:   17 nodes to be scored   (6564 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6597 eliminated genes)
## [1] "Significant BP terms for mistyrose module: 12"
## 
## Building most specific GOs .....
##  ( 9519 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 13352 GO terms and 30162 relations. )
## 
## Annotating nodes ...............
##  ( 6661 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 761 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 15:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  6 nodes to be scored    (0 eliminated genes)
## 
##   Level 13:  8 nodes to be scored    (65 eliminated genes)
## 
##   Level 12:  13 nodes to be scored   (247 eliminated genes)
## 
##   Level 11:  26 nodes to be scored   (844 eliminated genes)
## 
##   Level 10:  47 nodes to be scored   (1693 eliminated genes)
## 
##   Level 9:   68 nodes to be scored   (2113 eliminated genes)
## 
##   Level 8:   91 nodes to be scored   (2733 eliminated genes)
## 
##   Level 7:   118 nodes to be scored  (3343 eliminated genes)
## 
##   Level 6:   135 nodes to be scored  (4351 eliminated genes)
## 
##   Level 5:   125 nodes to be scored  (5394 eliminated genes)
## 
##   Level 4:   71 nodes to be scored   (6108 eliminated genes)
## 
##   Level 3:   38 nodes to be scored   (6417 eliminated genes)
## 
##   Level 2:   12 nodes to be scored   (6528 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6577 eliminated genes)
## [1] "Significant BP terms for peachpuff module: 12"
## 
## Building most specific GOs .....
##  ( 9519 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 13352 GO terms and 30162 relations. )
## 
## Annotating nodes ...............
##  ( 6661 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1871 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  9 nodes to be scored    (33 eliminated genes)
## 
##   Level 13:  22 nodes to be scored   (93 eliminated genes)
## 
##   Level 12:  39 nodes to be scored   (299 eliminated genes)
## 
##   Level 11:  77 nodes to be scored   (1296 eliminated genes)
## 
##   Level 10:  137 nodes to be scored  (2112 eliminated genes)
## 
##   Level 9:   218 nodes to be scored  (2729 eliminated genes)
## 
##   Level 8:   258 nodes to be scored  (3539 eliminated genes)
## 
##   Level 7:   328 nodes to be scored  (4518 eliminated genes)
## 
##   Level 6:   319 nodes to be scored  (5318 eliminated genes)
## 
##   Level 5:   243 nodes to be scored  (6003 eliminated genes)
## 
##   Level 4:   129 nodes to be scored  (6322 eliminated genes)
## 
##   Level 3:   68 nodes to be scored   (6497 eliminated genes)
## 
##   Level 2:   16 nodes to be scored   (6558 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6599 eliminated genes)
## [1] "Significant BP terms for rosybrown module: 12"
## 
## Building most specific GOs .....
##  ( 9519 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 13352 GO terms and 30162 relations. )
## 
## Annotating nodes ...............
##  ( 6661 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 2457 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  4 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  8 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  17 nodes to be scored   (62 eliminated genes)
## 
##   Level 13:  29 nodes to be scored   (160 eliminated genes)
## 
##   Level 12:  44 nodes to be scored   (449 eliminated genes)
## 
##   Level 11:  87 nodes to be scored   (1345 eliminated genes)
## 
##   Level 10:  185 nodes to be scored  (2033 eliminated genes)
## 
##   Level 9:   276 nodes to be scored  (2600 eliminated genes)
## 
##   Level 8:   377 nodes to be scored  (3491 eliminated genes)
## 
##   Level 7:   450 nodes to be scored  (4489 eliminated genes)
## 
##   Level 6:   427 nodes to be scored  (5413 eliminated genes)
## 
##   Level 5:   294 nodes to be scored  (6071 eliminated genes)
## 
##   Level 4:   165 nodes to be scored  (6396 eliminated genes)
## 
##   Level 3:   75 nodes to be scored   (6514 eliminated genes)
## 
##   Level 2:   18 nodes to be scored   (6566 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6599 eliminated genes)
## [1] "Significant BP terms for saddlebrown module: 75"
## 
## Building most specific GOs .....
##  ( 9519 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 13352 GO terms and 30162 relations. )
## 
## Annotating nodes ...............
##  ( 6661 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1617 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 15:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  8 nodes to be scored    (0 eliminated genes)
## 
##   Level 13:  24 nodes to be scored   (24 eliminated genes)
## 
##   Level 12:  35 nodes to be scored   (240 eliminated genes)
## 
##   Level 11:  67 nodes to be scored   (1302 eliminated genes)
## 
##   Level 10:  127 nodes to be scored  (2006 eliminated genes)
## 
##   Level 9:   173 nodes to be scored  (2570 eliminated genes)
## 
##   Level 8:   211 nodes to be scored  (3470 eliminated genes)
## 
##   Level 7:   259 nodes to be scored  (4220 eliminated genes)
## 
##   Level 6:   262 nodes to be scored  (5173 eliminated genes)
## 
##   Level 5:   233 nodes to be scored  (5764 eliminated genes)
## 
##   Level 4:   133 nodes to be scored  (6322 eliminated genes)
## 
##   Level 3:   66 nodes to be scored   (6507 eliminated genes)
## 
##   Level 2:   17 nodes to be scored   (6563 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6600 eliminated genes)
## [1] "Significant BP terms for sienna module: 20"

GOPlots <- list()

for(i in 1:length(modules)){
  if (!all(is.na(ResBP[[i]]$ResSel))) {
    Plot <- topGOBarplot(ResBP[[i]]$ResSel, terms=12, pvalTh=0.01, title=modules[i], palette=NULL)
    GOPlots$BP_Bar[[i]] <- Plot
    names(GOPlots$BP_Bar)[i] <- modules[i]
    }else{
      cat(modules[i], " module has no significant selected terms")
      next}
}

do.call(grid.arrange, c(GOPlots$BP_Bar, ncol = 3))

3.2 Molecular Function

ResMF <- list()

for(i in 1:length(modules)){
  MFann <- topGO::annFUN.org(whichOnto="MF", feasibleGenes=names(GeneVectors[[modules[i]]]), mapping="org.Hs.eg.db", ID="symbol") %>% topGO::inverseList()
  Res <- topGOResults(Genes=GeneVectors[[modules[i]]], gene2GO=MFann, ontology='MF', 
                      description=NULL, nodeSize=15, algorithm='weight01', 
                      statistic='fisher', EnTh=2, PvalTh=0.01, minTerms=12)
  print(paste('Significant MF terms for', modules[i], 'module:', dim(Res$ResSel)[1]))
  ResMF[[i]] <- Res
  names(ResMF)[i] <- modules[i]
  #write.table(Res$ResSel, file=paste0(OutputFolder, modules[i], '_MF.txt'), sep='\t', row.names=FALSE)
}
## 
## Building most specific GOs .....
##  ( 3027 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3520 GO terms and 4600 relations. )
## 
## Annotating nodes ...............
##  ( 6760 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 258 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   5 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   8 nodes to be scored    (452 eliminated genes)
## 
##   Level 7:   27 nodes to be scored   (1312 eliminated genes)
## 
##   Level 6:   47 nodes to be scored   (1472 eliminated genes)
## 
##   Level 5:   63 nodes to be scored   (1981 eliminated genes)
## 
##   Level 4:   59 nodes to be scored   (3356 eliminated genes)
## 
##   Level 3:   35 nodes to be scored   (4674 eliminated genes)
## 
##   Level 2:   12 nodes to be scored   (5300 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6565 eliminated genes)
## [1] "Significant MF terms for burlywood module: 20"
## 
## Building most specific GOs .....
##  ( 3027 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3520 GO terms and 4600 relations. )
## 
## Annotating nodes ...............
##  ( 6760 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 349 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  4 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   9 nodes to be scored    (57 eliminated genes)
## 
##   Level 8:   17 nodes to be scored   (527 eliminated genes)
## 
##   Level 7:   34 nodes to be scored   (1469 eliminated genes)
## 
##   Level 6:   58 nodes to be scored   (1696 eliminated genes)
## 
##   Level 5:   85 nodes to be scored   (2247 eliminated genes)
## 
##   Level 4:   87 nodes to be scored   (3719 eliminated genes)
## 
##   Level 3:   39 nodes to be scored   (4944 eliminated genes)
## 
##   Level 2:   13 nodes to be scored   (5507 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6694 eliminated genes)
## [1] "Significant MF terms for chocolate module: 12"
## 
## Building most specific GOs .....
##  ( 3027 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3520 GO terms and 4600 relations. )
## 
## Annotating nodes ...............
##  ( 6760 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 29 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 8:   1 nodes to be scored    (0 eliminated genes)
## 
##   Level 7:   4 nodes to be scored    (0 eliminated genes)
## 
##   Level 6:   4 nodes to be scored    (37 eliminated genes)
## 
##   Level 5:   6 nodes to be scored    (70 eliminated genes)
## 
##   Level 4:   6 nodes to be scored    (446 eliminated genes)
## 
##   Level 3:   5 nodes to be scored    (1864 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (2701 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6237 eliminated genes)
## [1] "Significant MF terms for darkgoldenrod module: 12"
## 
## Building most specific GOs .....
##  ( 3027 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3520 GO terms and 4600 relations. )
## 
## Annotating nodes ...............
##  ( 6760 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 334 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   12 nodes to be scored   (73 eliminated genes)
## 
##   Level 8:   12 nodes to be scored   (551 eliminated genes)
## 
##   Level 7:   31 nodes to be scored   (1459 eliminated genes)
## 
##   Level 6:   54 nodes to be scored   (1590 eliminated genes)
## 
##   Level 5:   87 nodes to be scored   (2167 eliminated genes)
## 
##   Level 4:   86 nodes to be scored   (3699 eliminated genes)
## 
##   Level 3:   31 nodes to be scored   (4937 eliminated genes)
## 
##   Level 2:   12 nodes to be scored   (5666 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6661 eliminated genes)
## [1] "Significant MF terms for dimgrey module: 12"
## 
## Building most specific GOs .....
##  ( 3027 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3520 GO terms and 4600 relations. )
## 
## Annotating nodes ...............
##  ( 6760 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 328 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  4 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   12 nodes to be scored   (73 eliminated genes)
## 
##   Level 8:   17 nodes to be scored   (535 eliminated genes)
## 
##   Level 7:   35 nodes to be scored   (1495 eliminated genes)
## 
##   Level 6:   58 nodes to be scored   (1694 eliminated genes)
## 
##   Level 5:   81 nodes to be scored   (2283 eliminated genes)
## 
##   Level 4:   75 nodes to be scored   (3610 eliminated genes)
## 
##   Level 3:   31 nodes to be scored   (4847 eliminated genes)
## 
##   Level 2:   11 nodes to be scored   (5620 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6680 eliminated genes)
## [1] "Significant MF terms for indianred module: 12"
## 
## Building most specific GOs .....
##  ( 3027 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3520 GO terms and 4600 relations. )
## 
## Annotating nodes ...............
##  ( 6760 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 269 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 9:   7 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   10 nodes to be scored   (0 eliminated genes)
## 
##   Level 7:   22 nodes to be scored   (872 eliminated genes)
## 
##   Level 6:   39 nodes to be scored   (1556 eliminated genes)
## 
##   Level 5:   70 nodes to be scored   (2191 eliminated genes)
## 
##   Level 4:   71 nodes to be scored   (3428 eliminated genes)
## 
##   Level 3:   34 nodes to be scored   (4849 eliminated genes)
## 
##   Level 2:   15 nodes to be scored   (5502 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6678 eliminated genes)
## [1] "Significant MF terms for lemonchiffon module: 12"
## 
## Building most specific GOs .....
##  ( 3027 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3520 GO terms and 4600 relations. )
## 
## Annotating nodes ...............
##  ( 6760 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 317 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  4 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   9 nodes to be scored    (45 eliminated genes)
## 
##   Level 8:   14 nodes to be scored   (553 eliminated genes)
## 
##   Level 7:   29 nodes to be scored   (1445 eliminated genes)
## 
##   Level 6:   53 nodes to be scored   (1645 eliminated genes)
## 
##   Level 5:   79 nodes to be scored   (2221 eliminated genes)
## 
##   Level 4:   80 nodes to be scored   (3637 eliminated genes)
## 
##   Level 3:   34 nodes to be scored   (4995 eliminated genes)
## 
##   Level 2:   12 nodes to be scored   (5653 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6679 eliminated genes)
## [1] "Significant MF terms for mistyrose module: 12"
## 
## Building most specific GOs .....
##  ( 3027 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3520 GO terms and 4600 relations. )
## 
## Annotating nodes ...............
##  ( 6760 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 168 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   6 nodes to be scored    (29 eliminated genes)
## 
##   Level 8:   8 nodes to be scored    (491 eliminated genes)
## 
##   Level 7:   20 nodes to be scored   (1354 eliminated genes)
## 
##   Level 6:   27 nodes to be scored   (1461 eliminated genes)
## 
##   Level 5:   33 nodes to be scored   (1932 eliminated genes)
## 
##   Level 4:   40 nodes to be scored   (2904 eliminated genes)
## 
##   Level 3:   21 nodes to be scored   (4180 eliminated genes)
## 
##   Level 2:   8 nodes to be scored    (5103 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6593 eliminated genes)
## [1] "Significant MF terms for peachpuff module: 12"
## 
## Building most specific GOs .....
##  ( 3027 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3520 GO terms and 4600 relations. )
## 
## Annotating nodes ...............
##  ( 6760 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 283 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   6 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   10 nodes to be scored   (452 eliminated genes)
## 
##   Level 7:   27 nodes to be scored   (1342 eliminated genes)
## 
##   Level 6:   54 nodes to be scored   (1505 eliminated genes)
## 
##   Level 5:   70 nodes to be scored   (2205 eliminated genes)
## 
##   Level 4:   69 nodes to be scored   (3610 eliminated genes)
## 
##   Level 3:   32 nodes to be scored   (4838 eliminated genes)
## 
##   Level 2:   13 nodes to be scored   (5541 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6682 eliminated genes)
## [1] "Significant MF terms for rosybrown module: 12"
## 
## Building most specific GOs .....
##  ( 3027 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3520 GO terms and 4600 relations. )
## 
## Annotating nodes ...............
##  ( 6760 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 283 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   8 nodes to be scored    (44 eliminated genes)
## 
##   Level 8:   11 nodes to be scored   (513 eliminated genes)
## 
##   Level 7:   22 nodes to be scored   (1349 eliminated genes)
## 
##   Level 6:   44 nodes to be scored   (1501 eliminated genes)
## 
##   Level 5:   70 nodes to be scored   (2189 eliminated genes)
## 
##   Level 4:   75 nodes to be scored   (3523 eliminated genes)
## 
##   Level 3:   34 nodes to be scored   (4965 eliminated genes)
## 
##   Level 2:   13 nodes to be scored   (5565 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6685 eliminated genes)
## [1] "Significant MF terms for saddlebrown module: 12"
## 
## Building most specific GOs .....
##  ( 3027 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3520 GO terms and 4600 relations. )
## 
## Annotating nodes ...............
##  ( 6760 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 224 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   5 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   6 nodes to be scored    (452 eliminated genes)
## 
##   Level 7:   13 nodes to be scored   (1319 eliminated genes)
## 
##   Level 6:   35 nodes to be scored   (1429 eliminated genes)
## 
##   Level 5:   59 nodes to be scored   (1560 eliminated genes)
## 
##   Level 4:   59 nodes to be scored   (2774 eliminated genes)
## 
##   Level 3:   33 nodes to be scored   (4795 eliminated genes)
## 
##   Level 2:   12 nodes to be scored   (5499 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6672 eliminated genes)
## [1] "Significant MF terms for sienna module: 12"

for(i in 1:length(modules)){
  if (!all(is.na(ResMF[[i]]$ResSel))) {
    Plot <- topGOBarplot(ResMF[[i]]$ResSel, terms=12, pvalTh=0.01, title=modules[i], palette=NULL)
    GOPlots$MF_Bar[[i]] <- Plot
    names(GOPlots$MF_Bar)[i] <- modules[i]
    }else{
      cat(modules[i], " module has no significant selected terms")
      next}
}

do.call(grid.arrange, c(GOPlots$MF_Bar, ncol = 3))

3.3 Cellular Component

ResCC <- list()

for(i in 1:length(modules)){
  CCann <- topGO::annFUN.org(whichOnto="CC", feasibleGenes=names(GeneVectors[[modules[i]]]), mapping="org.Hs.eg.db", ID="symbol") %>% topGO::inverseList()
  Res <- topGOResults(Genes=GeneVectors[[modules[i]]], gene2GO=CCann, ontology='CC', 
                      description=NULL, nodeSize=15, algorithm='weight01', 
                      statistic='fisher', EnTh=2, PvalTh=0.01, minTerms=12)
  print(paste('Significant CC terms for', modules[i], 'module:', dim(Res$ResSel)[1]))
  ResCC[[i]] <- Res
  names(ResCC)[i] <- modules[i]
  #write.table(Res$ResSel, file=paste0(OutputFolder, modules[i], '_CC-.txt'), sep='\t', row.names=FALSE)
}
## 
## Building most specific GOs .....
##  ( 1499 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1719 GO terms and 2908 relations. )
## 
## Annotating nodes ...............
##  ( 6981 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 225 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  10 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   26 nodes to be scored   (50 eliminated genes)
## 
##   Level 8:   38 nodes to be scored   (590 eliminated genes)
## 
##   Level 7:   32 nodes to be scored   (1704 eliminated genes)
## 
##   Level 6:   30 nodes to be scored   (3733 eliminated genes)
## 
##   Level 5:   31 nodes to be scored   (4624 eliminated genes)
## 
##   Level 4:   27 nodes to be scored   (5833 eliminated genes)
## 
##   Level 3:   26 nodes to be scored   (6568 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (6849 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6952 eliminated genes)
## [1] "Significant CC terms for burlywood module: 36"
## 
## Building most specific GOs .....
##  ( 1499 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1719 GO terms and 2908 relations. )
## 
## Annotating nodes ...............
##  ( 6981 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 376 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 12:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 11:  9 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  31 nodes to be scored   (20 eliminated genes)
## 
##   Level 9:   48 nodes to be scored   (265 eliminated genes)
## 
##   Level 8:   53 nodes to be scored   (1083 eliminated genes)
## 
##   Level 7:   64 nodes to be scored   (2229 eliminated genes)
## 
##   Level 6:   57 nodes to be scored   (3976 eliminated genes)
## 
##   Level 5:   47 nodes to be scored   (5011 eliminated genes)
## 
##   Level 4:   29 nodes to be scored   (5990 eliminated genes)
## 
##   Level 3:   34 nodes to be scored   (6646 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (6870 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6952 eliminated genes)
## [1] "Significant CC terms for chocolate module: 12"
## 
## Building most specific GOs .....
##  ( 1499 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1719 GO terms and 2908 relations. )
## 
## Annotating nodes ...............
##  ( 6981 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 41 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   3 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   4 nodes to be scored    (77 eliminated genes)
## 
##   Level 7:   3 nodes to be scored    (394 eliminated genes)
## 
##   Level 6:   7 nodes to be scored    (818 eliminated genes)
## 
##   Level 5:   7 nodes to be scored    (1138 eliminated genes)
## 
##   Level 4:   7 nodes to be scored    (1830 eliminated genes)
## 
##   Level 3:   7 nodes to be scored    (6323 eliminated genes)
## 
##   Level 2:   1 nodes to be scored    (6785 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6933 eliminated genes)
## [1] "Significant CC terms for darkgoldenrod module: 12"
## 
## Building most specific GOs .....
##  ( 1499 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1719 GO terms and 2908 relations. )
## 
## Annotating nodes ...............
##  ( 6981 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 351 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 12:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 11:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  22 nodes to be scored   (20 eliminated genes)
## 
##   Level 9:   46 nodes to be scored   (104 eliminated genes)
## 
##   Level 8:   57 nodes to be scored   (902 eliminated genes)
## 
##   Level 7:   50 nodes to be scored   (2253 eliminated genes)
## 
##   Level 6:   52 nodes to be scored   (3980 eliminated genes)
## 
##   Level 5:   53 nodes to be scored   (4859 eliminated genes)
## 
##   Level 4:   34 nodes to be scored   (5927 eliminated genes)
## 
##   Level 3:   30 nodes to be scored   (6650 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (6877 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6952 eliminated genes)
## [1] "Significant CC terms for dimgrey module: 12"
## 
## Building most specific GOs .....
##  ( 1499 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1719 GO terms and 2908 relations. )
## 
## Annotating nodes ...............
##  ( 6981 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 319 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  6 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  19 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   35 nodes to be scored   (146 eliminated genes)
## 
##   Level 8:   51 nodes to be scored   (855 eliminated genes)
## 
##   Level 7:   49 nodes to be scored   (2074 eliminated genes)
## 
##   Level 6:   53 nodes to be scored   (3941 eliminated genes)
## 
##   Level 5:   43 nodes to be scored   (4847 eliminated genes)
## 
##   Level 4:   28 nodes to be scored   (5941 eliminated genes)
## 
##   Level 3:   32 nodes to be scored   (6629 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (6876 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6952 eliminated genes)
## [1] "Significant CC terms for indianred module: 12"
## 
## Building most specific GOs .....
##  ( 1499 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1719 GO terms and 2908 relations. )
## 
## Annotating nodes ...............
##  ( 6981 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 341 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  11 nodes to be scored   (0 eliminated genes)
## 
##   Level 10:  31 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   45 nodes to be scored   (295 eliminated genes)
## 
##   Level 8:   50 nodes to be scored   (1150 eliminated genes)
## 
##   Level 7:   47 nodes to be scored   (2249 eliminated genes)
## 
##   Level 6:   47 nodes to be scored   (3975 eliminated genes)
## 
##   Level 5:   46 nodes to be scored   (4876 eliminated genes)
## 
##   Level 4:   34 nodes to be scored   (5895 eliminated genes)
## 
##   Level 3:   27 nodes to be scored   (6585 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (6850 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6952 eliminated genes)
## [1] "Significant CC terms for lemonchiffon module: 18"
## 
## Building most specific GOs .....
##  ( 1499 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1719 GO terms and 2908 relations. )
## 
## Annotating nodes ...............
##  ( 6981 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 322 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  4 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  19 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   46 nodes to be scored   (122 eliminated genes)
## 
##   Level 8:   48 nodes to be scored   (829 eliminated genes)
## 
##   Level 7:   50 nodes to be scored   (2067 eliminated genes)
## 
##   Level 6:   48 nodes to be scored   (3936 eliminated genes)
## 
##   Level 5:   46 nodes to be scored   (4938 eliminated genes)
## 
##   Level 4:   29 nodes to be scored   (5930 eliminated genes)
## 
##   Level 3:   29 nodes to be scored   (6637 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (6876 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6952 eliminated genes)
## [1] "Significant CC terms for mistyrose module: 12"
## 
## Building most specific GOs .....
##  ( 1499 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1719 GO terms and 2908 relations. )
## 
## Annotating nodes ...............
##  ( 6981 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 134 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   11 nodes to be scored   (57 eliminated genes)
## 
##   Level 8:   14 nodes to be scored   (279 eliminated genes)
## 
##   Level 7:   20 nodes to be scored   (908 eliminated genes)
## 
##   Level 6:   18 nodes to be scored   (3164 eliminated genes)
## 
##   Level 5:   20 nodes to be scored   (4319 eliminated genes)
## 
##   Level 4:   22 nodes to be scored   (5766 eliminated genes)
## 
##   Level 3:   19 nodes to be scored   (6522 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (6848 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6952 eliminated genes)
## [1] "Significant CC terms for peachpuff module: 12"
## 
## Building most specific GOs .....
##  ( 1499 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1719 GO terms and 2908 relations. )
## 
## Annotating nodes ...............
##  ( 6981 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 288 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  9 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  26 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   36 nodes to be scored   (248 eliminated genes)
## 
##   Level 8:   42 nodes to be scored   (1010 eliminated genes)
## 
##   Level 7:   44 nodes to be scored   (2059 eliminated genes)
## 
##   Level 6:   42 nodes to be scored   (3884 eliminated genes)
## 
##   Level 5:   34 nodes to be scored   (4863 eliminated genes)
## 
##   Level 4:   28 nodes to be scored   (5935 eliminated genes)
## 
##   Level 3:   24 nodes to be scored   (6611 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (6870 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6952 eliminated genes)
## [1] "Significant CC terms for rosybrown module: 12"
## 
## Building most specific GOs .....
##  ( 1499 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1719 GO terms and 2908 relations. )
## 
## Annotating nodes ...............
##  ( 6981 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 301 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  8 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  21 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   30 nodes to be scored   (210 eliminated genes)
## 
##   Level 8:   39 nodes to be scored   (928 eliminated genes)
## 
##   Level 7:   44 nodes to be scored   (1954 eliminated genes)
## 
##   Level 6:   52 nodes to be scored   (3900 eliminated genes)
## 
##   Level 5:   46 nodes to be scored   (4824 eliminated genes)
## 
##   Level 4:   28 nodes to be scored   (5940 eliminated genes)
## 
##   Level 3:   30 nodes to be scored   (6642 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (6869 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6952 eliminated genes)
## [1] "Significant CC terms for saddlebrown module: 12"
## 
## Building most specific GOs .....
##  ( 1499 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1719 GO terms and 2908 relations. )
## 
## Annotating nodes ...............
##  ( 6981 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 272 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  4 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  15 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   30 nodes to be scored   (161 eliminated genes)
## 
##   Level 8:   42 nodes to be scored   (726 eliminated genes)
## 
##   Level 7:   44 nodes to be scored   (1982 eliminated genes)
## 
##   Level 6:   44 nodes to be scored   (3778 eliminated genes)
## 
##   Level 5:   35 nodes to be scored   (4841 eliminated genes)
## 
##   Level 4:   29 nodes to be scored   (5923 eliminated genes)
## 
##   Level 3:   26 nodes to be scored   (6617 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (6870 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6952 eliminated genes)
## [1] "Significant CC terms for sienna module: 12"

for(i in 1:length(modules)){
  if (!all(is.na(ResCC[[i]]$ResSel))) {
    Plot <- topGOBarplot(ResCC[[i]]$ResSel, terms=12, pvalTh=0.01, title=modules[i], palette=NULL)
    GOPlots$CC_Bar[[i]] <- Plot
    names(GOPlots$CC_Bar)[i] <- modules[i]
    }else{
      cat(modules[i], " module has no significant selected terms")
      next}
}

do.call(grid.arrange, c(GOPlots$CC_Bar, ncol = 3))

4. Gene Ontology Analysis - hormones neurons

GeneVectors <- buildGeneVector(paths$hormones_Neurons)
modules <- names(GeneVectors)

4.1 Biological Process

ResBP <- list()

for(i in 1:length(modules)){
  BPann <- topGO::annFUN.org(whichOnto="BP", feasibleGenes=names(GeneVectors[[modules[i]]]), mapping="org.Hs.eg.db", ID="symbol") %>% topGO::inverseList()

  Res <- topGOResults(Genes=GeneVectors[[modules[i]]], gene2GO=BPann, ontology='BP', 
                      description=NULL, nodeSize=15, algorithm='weight01', 
                      statistic='fisher', EnTh=2, PvalTh=0.01, minTerms=12)
  print(paste('Significant BP terms for', modules[i], 'module:', dim(Res$ResSel)[1]))
  ResBP[[i]] <- Res
  names(ResBP)[i] <- modules[i]
  #write.table(Res$ResSel, file=paste0(OutputFolder, modules[i], '_BP.txt'), sep='\t', row.names=FALSE)
}
## 
## Building most specific GOs .....
##  ( 10713 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 14351 GO terms and 32449 relations. )
## 
## Annotating nodes ...............
##  ( 9307 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1573 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  7 nodes to be scored    (19 eliminated genes)
## 
##   Level 13:  21 nodes to be scored   (61 eliminated genes)
## 
##   Level 12:  30 nodes to be scored   (428 eliminated genes)
## 
##   Level 11:  52 nodes to be scored   (1691 eliminated genes)
## 
##   Level 10:  104 nodes to be scored  (2719 eliminated genes)
## 
##   Level 9:   171 nodes to be scored  (3295 eliminated genes)
## 
##   Level 8:   224 nodes to be scored  (4287 eliminated genes)
## 
##   Level 7:   277 nodes to be scored  (5683 eliminated genes)
## 
##   Level 6:   274 nodes to be scored  (7048 eliminated genes)
## 
##   Level 5:   215 nodes to be scored  (8089 eliminated genes)
## 
##   Level 4:   122 nodes to be scored  (8814 eliminated genes)
## 
##   Level 3:   58 nodes to be scored   (9051 eliminated genes)
## 
##   Level 2:   14 nodes to be scored   (9164 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9192 eliminated genes)
## [1] "Significant BP terms for bisque module: 12"
## 
## Building most specific GOs .....
##  ( 10713 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 14351 GO terms and 32449 relations. )
## 
## Annotating nodes ...............
##  ( 9307 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1747 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 15:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  9 nodes to be scored    (0 eliminated genes)
## 
##   Level 13:  22 nodes to be scored   (70 eliminated genes)
## 
##   Level 12:  44 nodes to be scored   (396 eliminated genes)
## 
##   Level 11:  80 nodes to be scored   (1609 eliminated genes)
## 
##   Level 10:  127 nodes to be scored  (2870 eliminated genes)
## 
##   Level 9:   178 nodes to be scored  (3587 eliminated genes)
## 
##   Level 8:   222 nodes to be scored  (4336 eliminated genes)
## 
##   Level 7:   299 nodes to be scored  (5758 eliminated genes)
## 
##   Level 6:   298 nodes to be scored  (7202 eliminated genes)
## 
##   Level 5:   245 nodes to be scored  (8208 eliminated genes)
## 
##   Level 4:   139 nodes to be scored  (8851 eliminated genes)
## 
##   Level 3:   65 nodes to be scored   (9074 eliminated genes)
## 
##   Level 2:   16 nodes to be scored   (9170 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9194 eliminated genes)
## [1] "Significant BP terms for chocolate module: 12"
## 
## Building most specific GOs .....
##  ( 10713 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 14351 GO terms and 32449 relations. )
## 
## Annotating nodes ...............
##  ( 9307 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 2686 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 17:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 16:  6 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  13 nodes to be scored   (21 eliminated genes)
## 
##   Level 14:  17 nodes to be scored   (107 eliminated genes)
## 
##   Level 13:  31 nodes to be scored   (227 eliminated genes)
## 
##   Level 12:  56 nodes to be scored   (556 eliminated genes)
## 
##   Level 11:  121 nodes to be scored  (1813 eliminated genes)
## 
##   Level 10:  210 nodes to be scored  (2922 eliminated genes)
## 
##   Level 9:   326 nodes to be scored  (3647 eliminated genes)
## 
##   Level 8:   406 nodes to be scored  (4906 eliminated genes)
## 
##   Level 7:   484 nodes to be scored  (6480 eliminated genes)
## 
##   Level 6:   453 nodes to be scored  (7761 eliminated genes)
## 
##   Level 5:   304 nodes to be scored  (8476 eliminated genes)
## 
##   Level 4:   168 nodes to be scored  (8937 eliminated genes)
## 
##   Level 3:   73 nodes to be scored   (9101 eliminated genes)
## 
##   Level 2:   16 nodes to be scored   (9175 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9203 eliminated genes)
## [1] "Significant BP terms for darkgrey module: 44"
## 
## Building most specific GOs .....
##  ( 10713 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 14351 GO terms and 32449 relations. )
## 
## Annotating nodes ...............
##  ( 9307 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 2247 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  14 nodes to be scored   (32 eliminated genes)
## 
##   Level 13:  30 nodes to be scored   (170 eliminated genes)
## 
##   Level 12:  48 nodes to be scored   (497 eliminated genes)
## 
##   Level 11:  100 nodes to be scored  (1880 eliminated genes)
## 
##   Level 10:  185 nodes to be scored  (2893 eliminated genes)
## 
##   Level 9:   260 nodes to be scored  (3773 eliminated genes)
## 
##   Level 8:   303 nodes to be scored  (4852 eliminated genes)
## 
##   Level 7:   382 nodes to be scored  (6448 eliminated genes)
## 
##   Level 6:   389 nodes to be scored  (7611 eliminated genes)
## 
##   Level 5:   278 nodes to be scored  (8373 eliminated genes)
## 
##   Level 4:   155 nodes to be scored  (8923 eliminated genes)
## 
##   Level 3:   78 nodes to be scored   (9103 eliminated genes)
## 
##   Level 2:   18 nodes to be scored   (9175 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9206 eliminated genes)
## [1] "Significant BP terms for darkred module: 12"
## 
## Building most specific GOs .....
##  ( 10713 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 14351 GO terms and 32449 relations. )
## 
## Annotating nodes ...............
##  ( 9307 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1849 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  11 nodes to be scored   (0 eliminated genes)
## 
##   Level 14:  15 nodes to be scored   (36 eliminated genes)
## 
##   Level 13:  29 nodes to be scored   (243 eliminated genes)
## 
##   Level 12:  38 nodes to be scored   (465 eliminated genes)
## 
##   Level 11:  72 nodes to be scored   (1762 eliminated genes)
## 
##   Level 10:  134 nodes to be scored  (2726 eliminated genes)
## 
##   Level 9:   197 nodes to be scored  (3654 eliminated genes)
## 
##   Level 8:   252 nodes to be scored  (4722 eliminated genes)
## 
##   Level 7:   325 nodes to be scored  (6023 eliminated genes)
## 
##   Level 6:   318 nodes to be scored  (7361 eliminated genes)
## 
##   Level 5:   237 nodes to be scored  (8222 eliminated genes)
## 
##   Level 4:   138 nodes to be scored  (8868 eliminated genes)
## 
##   Level 3:   65 nodes to be scored   (9066 eliminated genes)
## 
##   Level 2:   16 nodes to be scored   (9157 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9207 eliminated genes)
## [1] "Significant BP terms for darksalmon module: 25"
## 
## Building most specific GOs .....
##  ( 10713 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 14351 GO terms and 32449 relations. )
## 
## Annotating nodes ...............
##  ( 9307 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 2095 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 17:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 16:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  8 nodes to be scored    (20 eliminated genes)
## 
##   Level 14:  11 nodes to be scored   (52 eliminated genes)
## 
##   Level 13:  25 nodes to be scored   (182 eliminated genes)
## 
##   Level 12:  39 nodes to be scored   (411 eliminated genes)
## 
##   Level 11:  98 nodes to be scored   (1749 eliminated genes)
## 
##   Level 10:  169 nodes to be scored  (2759 eliminated genes)
## 
##   Level 9:   254 nodes to be scored  (3744 eliminated genes)
## 
##   Level 8:   289 nodes to be scored  (4823 eliminated genes)
## 
##   Level 7:   351 nodes to be scored  (6080 eliminated genes)
## 
##   Level 6:   356 nodes to be scored  (7329 eliminated genes)
## 
##   Level 5:   267 nodes to be scored  (8224 eliminated genes)
## 
##   Level 4:   140 nodes to be scored  (8866 eliminated genes)
## 
##   Level 3:   67 nodes to be scored   (9086 eliminated genes)
## 
##   Level 2:   16 nodes to be scored   (9160 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9206 eliminated genes)
## [1] "Significant BP terms for firebrick module: 15"
## 
## Building most specific GOs .....
##  ( 10713 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 14351 GO terms and 32449 relations. )
## 
## Annotating nodes ...............
##  ( 9307 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1368 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 14:  4 nodes to be scored    (0 eliminated genes)
## 
##   Level 13:  20 nodes to be scored   (0 eliminated genes)
## 
##   Level 12:  30 nodes to be scored   (175 eliminated genes)
## 
##   Level 11:  55 nodes to be scored   (1698 eliminated genes)
## 
##   Level 10:  102 nodes to be scored  (2658 eliminated genes)
## 
##   Level 9:   144 nodes to be scored  (3472 eliminated genes)
## 
##   Level 8:   184 nodes to be scored  (4677 eliminated genes)
## 
##   Level 7:   230 nodes to be scored  (5742 eliminated genes)
## 
##   Level 6:   230 nodes to be scored  (7261 eliminated genes)
## 
##   Level 5:   189 nodes to be scored  (8184 eliminated genes)
## 
##   Level 4:   104 nodes to be scored  (8688 eliminated genes)
## 
##   Level 3:   59 nodes to be scored   (9035 eliminated genes)
## 
##   Level 2:   16 nodes to be scored   (9152 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9199 eliminated genes)
## [1] "Significant BP terms for gainsboro module: 19"
## 
## Building most specific GOs .....
##  ( 10713 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 14351 GO terms and 32449 relations. )
## 
## Annotating nodes ...............
##  ( 9307 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 2391 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 18:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 17:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 16:  4 nodes to be scored    (15 eliminated genes)
## 
##   Level 15:  14 nodes to be scored   (40 eliminated genes)
## 
##   Level 14:  18 nodes to be scored   (76 eliminated genes)
## 
##   Level 13:  34 nodes to be scored   (236 eliminated genes)
## 
##   Level 12:  58 nodes to be scored   (587 eliminated genes)
## 
##   Level 11:  119 nodes to be scored  (1907 eliminated genes)
## 
##   Level 10:  185 nodes to be scored  (3051 eliminated genes)
## 
##   Level 9:   276 nodes to be scored  (3919 eliminated genes)
## 
##   Level 8:   347 nodes to be scored  (4962 eliminated genes)
## 
##   Level 7:   413 nodes to be scored  (6338 eliminated genes)
## 
##   Level 6:   393 nodes to be scored  (7603 eliminated genes)
## 
##   Level 5:   279 nodes to be scored  (8400 eliminated genes)
## 
##   Level 4:   159 nodes to be scored  (8913 eliminated genes)
## 
##   Level 3:   72 nodes to be scored   (9102 eliminated genes)
## 
##   Level 2:   16 nodes to be scored   (9177 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9202 eliminated genes)
## [1] "Significant BP terms for lightcoral module: 25"
## 
## Building most specific GOs .....
##  ( 10713 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 14351 GO terms and 32449 relations. )
## 
## Annotating nodes ...............
##  ( 9307 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 2467 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 18:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 17:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 16:  2 nodes to be scored    (15 eliminated genes)
## 
##   Level 15:  7 nodes to be scored    (20 eliminated genes)
## 
##   Level 14:  16 nodes to be scored   (46 eliminated genes)
## 
##   Level 13:  37 nodes to be scored   (192 eliminated genes)
## 
##   Level 12:  63 nodes to be scored   (660 eliminated genes)
## 
##   Level 11:  125 nodes to be scored  (1968 eliminated genes)
## 
##   Level 10:  219 nodes to be scored  (3082 eliminated genes)
## 
##   Level 9:   314 nodes to be scored  (4079 eliminated genes)
## 
##   Level 8:   359 nodes to be scored  (5395 eliminated genes)
## 
##   Level 7:   414 nodes to be scored  (6728 eliminated genes)
## 
##   Level 6:   392 nodes to be scored  (7839 eliminated genes)
## 
##   Level 5:   280 nodes to be scored  (8468 eliminated genes)
## 
##   Level 4:   150 nodes to be scored  (8930 eliminated genes)
## 
##   Level 3:   69 nodes to be scored   (9104 eliminated genes)
## 
##   Level 2:   17 nodes to be scored   (9175 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9206 eliminated genes)
## [1] "Significant BP terms for lightsalmon module: 23"
## 
## Building most specific GOs .....
##  ( 10713 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 14351 GO terms and 32449 relations. )
## 
## Annotating nodes ...............
##  ( 9307 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1998 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 18:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 17:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 16:  3 nodes to be scored    (15 eliminated genes)
## 
##   Level 15:  6 nodes to be scored    (20 eliminated genes)
## 
##   Level 14:  12 nodes to be scored   (39 eliminated genes)
## 
##   Level 13:  30 nodes to be scored   (129 eliminated genes)
## 
##   Level 12:  55 nodes to be scored   (426 eliminated genes)
## 
##   Level 11:  100 nodes to be scored  (1898 eliminated genes)
## 
##   Level 10:  159 nodes to be scored  (3087 eliminated genes)
## 
##   Level 9:   217 nodes to be scored  (3944 eliminated genes)
## 
##   Level 8:   262 nodes to be scored  (4976 eliminated genes)
## 
##   Level 7:   326 nodes to be scored  (6277 eliminated genes)
## 
##   Level 6:   328 nodes to be scored  (7421 eliminated genes)
## 
##   Level 5:   259 nodes to be scored  (8330 eliminated genes)
## 
##   Level 4:   151 nodes to be scored  (8878 eliminated genes)
## 
##   Level 3:   72 nodes to be scored   (9093 eliminated genes)
## 
##   Level 2:   15 nodes to be scored   (9172 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9206 eliminated genes)
## [1] "Significant BP terms for maroon module: 24"
## 
## Building most specific GOs .....
##  ( 10713 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 14351 GO terms and 32449 relations. )
## 
## Annotating nodes ...............
##  ( 9307 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 2342 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 17:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 16:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  5 nodes to be scored    (20 eliminated genes)
## 
##   Level 14:  14 nodes to be scored   (39 eliminated genes)
## 
##   Level 13:  28 nodes to be scored   (108 eliminated genes)
## 
##   Level 12:  55 nodes to be scored   (451 eliminated genes)
## 
##   Level 11:  116 nodes to be scored  (1839 eliminated genes)
## 
##   Level 10:  203 nodes to be scored  (3020 eliminated genes)
## 
##   Level 9:   299 nodes to be scored  (3996 eliminated genes)
## 
##   Level 8:   347 nodes to be scored  (5043 eliminated genes)
## 
##   Level 7:   395 nodes to be scored  (6454 eliminated genes)
## 
##   Level 6:   367 nodes to be scored  (7705 eliminated genes)
## 
##   Level 5:   279 nodes to be scored  (8382 eliminated genes)
## 
##   Level 4:   143 nodes to be scored  (8895 eliminated genes)
## 
##   Level 3:   70 nodes to be scored   (9093 eliminated genes)
## 
##   Level 2:   16 nodes to be scored   (9175 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9206 eliminated genes)
## [1] "Significant BP terms for orangered module: 19"
## 
## Building most specific GOs .....
##  ( 10713 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 14351 GO terms and 32449 relations. )
## 
## Annotating nodes ...............
##  ( 9307 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1899 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  6 nodes to be scored    (30 eliminated genes)
## 
##   Level 13:  26 nodes to be scored   (45 eliminated genes)
## 
##   Level 12:  48 nodes to be scored   (238 eliminated genes)
## 
##   Level 11:  84 nodes to be scored   (1776 eliminated genes)
## 
##   Level 10:  145 nodes to be scored  (2948 eliminated genes)
## 
##   Level 9:   226 nodes to be scored  (3947 eliminated genes)
## 
##   Level 8:   254 nodes to be scored  (5067 eliminated genes)
## 
##   Level 7:   319 nodes to be scored  (6165 eliminated genes)
## 
##   Level 6:   320 nodes to be scored  (7387 eliminated genes)
## 
##   Level 5:   241 nodes to be scored  (8282 eliminated genes)
## 
##   Level 4:   143 nodes to be scored  (8882 eliminated genes)
## 
##   Level 3:   67 nodes to be scored   (9079 eliminated genes)
## 
##   Level 2:   16 nodes to be scored   (9171 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9205 eliminated genes)
## [1] "Significant BP terms for peru module: 23"
## 
## Building most specific GOs .....
##  ( 10713 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 14351 GO terms and 32449 relations. )
## 
## Annotating nodes ...............
##  ( 9307 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 236 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   11 nodes to be scored   (92 eliminated genes)
## 
##   Level 8:   14 nodes to be scored   (272 eliminated genes)
## 
##   Level 7:   33 nodes to be scored   (661 eliminated genes)
## 
##   Level 6:   39 nodes to be scored   (1451 eliminated genes)
## 
##   Level 5:   46 nodes to be scored   (3212 eliminated genes)
## 
##   Level 4:   41 nodes to be scored   (5369 eliminated genes)
## 
##   Level 3:   30 nodes to be scored   (7388 eliminated genes)
## 
##   Level 2:   13 nodes to be scored   (8986 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9132 eliminated genes)
## [1] "Significant BP terms for red module: 12"
## 
## Building most specific GOs .....
##  ( 10713 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 14351 GO terms and 32449 relations. )
## 
## Annotating nodes ...............
##  ( 9307 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 2339 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 18:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 17:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 16:  1 nodes to be scored    (15 eliminated genes)
## 
##   Level 15:  14 nodes to be scored   (20 eliminated genes)
## 
##   Level 14:  17 nodes to be scored   (21 eliminated genes)
## 
##   Level 13:  29 nodes to be scored   (260 eliminated genes)
## 
##   Level 12:  53 nodes to be scored   (597 eliminated genes)
## 
##   Level 11:  122 nodes to be scored  (1868 eliminated genes)
## 
##   Level 10:  212 nodes to be scored  (2993 eliminated genes)
## 
##   Level 9:   274 nodes to be scored  (3837 eliminated genes)
## 
##   Level 8:   328 nodes to be scored  (5160 eliminated genes)
## 
##   Level 7:   386 nodes to be scored  (6420 eliminated genes)
## 
##   Level 6:   382 nodes to be scored  (7727 eliminated genes)
## 
##   Level 5:   278 nodes to be scored  (8463 eliminated genes)
## 
##   Level 4:   149 nodes to be scored  (8919 eliminated genes)
## 
##   Level 3:   75 nodes to be scored   (9098 eliminated genes)
## 
##   Level 2:   16 nodes to be scored   (9177 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9207 eliminated genes)
## [1] "Significant BP terms for snow module: 19"

GOPlots <- list()

for(i in 1:length(modules)){
  if (!all(is.na(ResBP[[i]]$ResSel))) {
    Plot <- topGOBarplot(ResBP[[i]]$ResSel, terms=12, pvalTh=0.01, title=modules[i], palette=NULL)
    GOPlots$BP_Bar[[i]] <- Plot
    names(GOPlots$BP_Bar)[i] <- modules[i]
    }else{
      cat(modules[i], " module has no significant selected terms")
      next}
}

do.call(grid.arrange, c(GOPlots$BP_Bar, ncol = 3))

4.2 Molecular Function

ResMF <- list()

for(i in 1:length(modules)){
  MFann <- topGO::annFUN.org(whichOnto="MF", feasibleGenes=names(GeneVectors[[modules[i]]]), mapping="org.Hs.eg.db", ID="symbol") %>% topGO::inverseList()
  Res <- topGOResults(Genes=GeneVectors[[modules[i]]], gene2GO=MFann, ontology='MF', 
                      description=NULL, nodeSize=15, algorithm='weight01', 
                      statistic='fisher', EnTh=2, PvalTh=0.01, minTerms=12)
  print(paste('Significant MF terms for', modules[i], 'module:', dim(Res$ResSel)[1]))
  ResMF[[i]] <- Res
  names(ResMF)[i] <- modules[i]
  #write.table(Res$ResSel, file=paste0(OutputFolder, modules[i], '_MF.txt'), sep='\t', row.names=FALSE)
}
## 
## Building most specific GOs .....
##  ( 3666 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4159 GO terms and 5411 relations. )
## 
## Annotating nodes ...............
##  ( 9511 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 232 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   5 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   9 nodes to be scored    (638 eliminated genes)
## 
##   Level 7:   21 nodes to be scored   (1659 eliminated genes)
## 
##   Level 6:   37 nodes to be scored   (2047 eliminated genes)
## 
##   Level 5:   57 nodes to be scored   (2805 eliminated genes)
## 
##   Level 4:   63 nodes to be scored   (4356 eliminated genes)
## 
##   Level 3:   28 nodes to be scored   (6771 eliminated genes)
## 
##   Level 2:   10 nodes to be scored   (7792 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9384 eliminated genes)
## [1] "Significant MF terms for bisque module: 12"
## 
## Building most specific GOs .....
##  ( 3666 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4159 GO terms and 5411 relations. )
## 
## Annotating nodes ...............
##  ( 9511 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 258 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   8 nodes to be scored    (62 eliminated genes)
## 
##   Level 8:   19 nodes to be scored   (743 eliminated genes)
## 
##   Level 7:   28 nodes to be scored   (1769 eliminated genes)
## 
##   Level 6:   41 nodes to be scored   (2320 eliminated genes)
## 
##   Level 5:   58 nodes to be scored   (3010 eliminated genes)
## 
##   Level 4:   61 nodes to be scored   (4725 eliminated genes)
## 
##   Level 3:   26 nodes to be scored   (6811 eliminated genes)
## 
##   Level 2:   10 nodes to be scored   (7739 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9372 eliminated genes)
## [1] "Significant MF terms for chocolate module: 12"
## 
## Building most specific GOs .....
##  ( 3666 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4159 GO terms and 5411 relations. )
## 
## Annotating nodes ...............
##  ( 9511 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 296 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   6 nodes to be scored    (28 eliminated genes)
## 
##   Level 8:   12 nodes to be scored   (638 eliminated genes)
## 
##   Level 7:   24 nodes to be scored   (1864 eliminated genes)
## 
##   Level 6:   51 nodes to be scored   (2150 eliminated genes)
## 
##   Level 5:   81 nodes to be scored   (3165 eliminated genes)
## 
##   Level 4:   79 nodes to be scored   (4966 eliminated genes)
## 
##   Level 3:   32 nodes to be scored   (6997 eliminated genes)
## 
##   Level 2:   8 nodes to be scored    (7822 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9392 eliminated genes)
## [1] "Significant MF terms for darkgrey module: 12"
## 
## Building most specific GOs .....
##  ( 3666 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4159 GO terms and 5411 relations. )
## 
## Annotating nodes ...............
##  ( 9511 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 337 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   9 nodes to be scored    (37 eliminated genes)
## 
##   Level 8:   14 nodes to be scored   (718 eliminated genes)
## 
##   Level 7:   33 nodes to be scored   (1759 eliminated genes)
## 
##   Level 6:   64 nodes to be scored   (1946 eliminated genes)
## 
##   Level 5:   78 nodes to be scored   (2990 eliminated genes)
## 
##   Level 4:   86 nodes to be scored   (5205 eliminated genes)
## 
##   Level 3:   35 nodes to be scored   (6884 eliminated genes)
## 
##   Level 2:   11 nodes to be scored   (7853 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9388 eliminated genes)
## [1] "Significant MF terms for darkred module: 12"
## 
## Building most specific GOs .....
##  ( 3666 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4159 GO terms and 5411 relations. )
## 
## Annotating nodes ...............
##  ( 9511 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 288 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  7 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   12 nodes to be scored   (53 eliminated genes)
## 
##   Level 8:   16 nodes to be scored   (807 eliminated genes)
## 
##   Level 7:   24 nodes to be scored   (1832 eliminated genes)
## 
##   Level 6:   45 nodes to be scored   (2260 eliminated genes)
## 
##   Level 5:   73 nodes to be scored   (3010 eliminated genes)
## 
##   Level 4:   69 nodes to be scored   (4723 eliminated genes)
## 
##   Level 3:   29 nodes to be scored   (6905 eliminated genes)
## 
##   Level 2:   10 nodes to be scored   (7835 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9384 eliminated genes)
## [1] "Significant MF terms for darksalmon module: 12"
## 
## Building most specific GOs .....
##  ( 3666 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4159 GO terms and 5411 relations. )
## 
## Annotating nodes ...............
##  ( 9511 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 300 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   10 nodes to be scored   (37 eliminated genes)
## 
##   Level 8:   16 nodes to be scored   (763 eliminated genes)
## 
##   Level 7:   27 nodes to be scored   (1992 eliminated genes)
## 
##   Level 6:   52 nodes to be scored   (2207 eliminated genes)
## 
##   Level 5:   67 nodes to be scored   (2838 eliminated genes)
## 
##   Level 4:   79 nodes to be scored   (4951 eliminated genes)
## 
##   Level 3:   32 nodes to be scored   (6825 eliminated genes)
## 
##   Level 2:   10 nodes to be scored   (7843 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9390 eliminated genes)
## [1] "Significant MF terms for firebrick module: 12"
## 
## Building most specific GOs .....
##  ( 3666 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4159 GO terms and 5411 relations. )
## 
## Annotating nodes ...............
##  ( 9511 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 253 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   9 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   10 nodes to be scored   (638 eliminated genes)
## 
##   Level 7:   21 nodes to be scored   (1859 eliminated genes)
## 
##   Level 6:   41 nodes to be scored   (2029 eliminated genes)
## 
##   Level 5:   63 nodes to be scored   (2890 eliminated genes)
## 
##   Level 4:   65 nodes to be scored   (4326 eliminated genes)
## 
##   Level 3:   29 nodes to be scored   (6538 eliminated genes)
## 
##   Level 2:   13 nodes to be scored   (7581 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9319 eliminated genes)
## [1] "Significant MF terms for gainsboro module: 12"
## 
## Building most specific GOs .....
##  ( 3666 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4159 GO terms and 5411 relations. )
## 
## Annotating nodes ...............
##  ( 9511 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 359 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  4 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  7 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   15 nodes to be scored   (73 eliminated genes)
## 
##   Level 8:   18 nodes to be scored   (801 eliminated genes)
## 
##   Level 7:   32 nodes to be scored   (2028 eliminated genes)
## 
##   Level 6:   65 nodes to be scored   (2348 eliminated genes)
## 
##   Level 5:   98 nodes to be scored   (3089 eliminated genes)
## 
##   Level 4:   78 nodes to be scored   (5360 eliminated genes)
## 
##   Level 3:   32 nodes to be scored   (7284 eliminated genes)
## 
##   Level 2:   9 nodes to be scored    (7958 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9397 eliminated genes)
## [1] "Significant MF terms for lightcoral module: 13"
## 
## Building most specific GOs .....
##  ( 3666 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4159 GO terms and 5411 relations. )
## 
## Annotating nodes ...............
##  ( 9511 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 393 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  6 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   16 nodes to be scored   (60 eliminated genes)
## 
##   Level 8:   26 nodes to be scored   (784 eliminated genes)
## 
##   Level 7:   47 nodes to be scored   (2025 eliminated genes)
## 
##   Level 6:   65 nodes to be scored   (2395 eliminated genes)
## 
##   Level 5:   93 nodes to be scored   (3246 eliminated genes)
## 
##   Level 4:   90 nodes to be scored   (5217 eliminated genes)
## 
##   Level 3:   33 nodes to be scored   (7123 eliminated genes)
## 
##   Level 2:   13 nodes to be scored   (7981 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9367 eliminated genes)
## [1] "Significant MF terms for lightsalmon module: 12"
## 
## Building most specific GOs .....
##  ( 3666 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4159 GO terms and 5411 relations. )
## 
## Annotating nodes ...............
##  ( 9511 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 320 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   10 nodes to be scored   (0 eliminated genes)
## 
##   Level 8:   13 nodes to be scored   (676 eliminated genes)
## 
##   Level 7:   29 nodes to be scored   (1935 eliminated genes)
## 
##   Level 6:   53 nodes to be scored   (2159 eliminated genes)
## 
##   Level 5:   81 nodes to be scored   (3137 eliminated genes)
## 
##   Level 4:   81 nodes to be scored   (4919 eliminated genes)
## 
##   Level 3:   36 nodes to be scored   (6898 eliminated genes)
## 
##   Level 2:   13 nodes to be scored   (7778 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9402 eliminated genes)
## [1] "Significant MF terms for maroon module: 12"
## 
## Building most specific GOs .....
##  ( 3666 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4159 GO terms and 5411 relations. )
## 
## Annotating nodes ...............
##  ( 9511 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 319 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   11 nodes to be scored   (0 eliminated genes)
## 
##   Level 8:   18 nodes to be scored   (675 eliminated genes)
## 
##   Level 7:   35 nodes to be scored   (1962 eliminated genes)
## 
##   Level 6:   55 nodes to be scored   (2202 eliminated genes)
## 
##   Level 5:   77 nodes to be scored   (2960 eliminated genes)
## 
##   Level 4:   79 nodes to be scored   (4997 eliminated genes)
## 
##   Level 3:   30 nodes to be scored   (6751 eliminated genes)
## 
##   Level 2:   10 nodes to be scored   (7751 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9298 eliminated genes)
## [1] "Significant MF terms for orangered module: 12"
## 
## Building most specific GOs .....
##  ( 3666 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4159 GO terms and 5411 relations. )
## 
## Annotating nodes ...............
##  ( 9511 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 299 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   9 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   15 nodes to be scored   (638 eliminated genes)
## 
##   Level 7:   29 nodes to be scored   (1873 eliminated genes)
## 
##   Level 6:   54 nodes to be scored   (2145 eliminated genes)
## 
##   Level 5:   72 nodes to be scored   (2778 eliminated genes)
## 
##   Level 4:   75 nodes to be scored   (5020 eliminated genes)
## 
##   Level 3:   31 nodes to be scored   (6635 eliminated genes)
## 
##   Level 2:   12 nodes to be scored   (7581 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9307 eliminated genes)
## [1] "Significant MF terms for peru module: 12"
## 
## Building most specific GOs .....
##  ( 3666 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4159 GO terms and 5411 relations. )
## 
## Annotating nodes ...............
##  ( 9511 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 48 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 9:   2 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   2 nodes to be scored    (0 eliminated genes)
## 
##   Level 7:   3 nodes to be scored    (220 eliminated genes)
## 
##   Level 6:   6 nodes to be scored    (260 eliminated genes)
## 
##   Level 5:   8 nodes to be scored    (1119 eliminated genes)
## 
##   Level 4:   11 nodes to be scored   (1692 eliminated genes)
## 
##   Level 3:   11 nodes to be scored   (3807 eliminated genes)
## 
##   Level 2:   4 nodes to be scored    (5044 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (8906 eliminated genes)
## [1] "Significant MF terms for red module: 12"
## 
## Building most specific GOs .....
##  ( 3666 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 4159 GO terms and 5411 relations. )
## 
## Annotating nodes ...............
##  ( 9511 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 340 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   10 nodes to be scored   (28 eliminated genes)
## 
##   Level 8:   24 nodes to be scored   (670 eliminated genes)
## 
##   Level 7:   41 nodes to be scored   (1915 eliminated genes)
## 
##   Level 6:   62 nodes to be scored   (2425 eliminated genes)
## 
##   Level 5:   72 nodes to be scored   (3189 eliminated genes)
## 
##   Level 4:   81 nodes to be scored   (5088 eliminated genes)
## 
##   Level 3:   33 nodes to be scored   (6843 eliminated genes)
## 
##   Level 2:   12 nodes to be scored   (7825 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9399 eliminated genes)
## [1] "Significant MF terms for snow module: 12"

for(i in 1:length(modules)){
  if (!all(is.na(ResMF[[i]]$ResSel))) {
    Plot <- topGOBarplot(ResMF[[i]]$ResSel, terms=12, pvalTh=0.01, title=modules[i], palette=NULL)
    GOPlots$MF_Bar[[i]] <- Plot
    names(GOPlots$MF_Bar)[i] <- modules[i]
    }else{
      cat(modules[i], " module has no significant selected terms")
      next}
}

do.call(grid.arrange, c(GOPlots$MF_Bar, ncol = 3))

4.3 Cellular Component

ResCC <- list()

for(i in 1:length(modules)){
  CCann <- topGO::annFUN.org(whichOnto="CC", feasibleGenes=names(GeneVectors[[modules[i]]]), mapping="org.Hs.eg.db", ID="symbol") %>% topGO::inverseList()
  Res <- topGOResults(Genes=GeneVectors[[modules[i]]], gene2GO=CCann, ontology='CC', 
                      description=NULL, nodeSize=15, algorithm='weight01', 
                      statistic='fisher', EnTh=2, PvalTh=0.01, minTerms=12)
  print(paste('Significant CC terms for', modules[i], 'module:', dim(Res$ResSel)[1]))
  ResCC[[i]] <- Res
  names(ResCC)[i] <- modules[i]
  #write.table(Res$ResSel, file=paste0(OutputFolder, modules[i], '_CC-.txt'), sep='\t', row.names=FALSE)
}
## 
## Building most specific GOs .....
##  ( 1654 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1851 GO terms and 3123 relations. )
## 
## Annotating nodes ...............
##  ( 9746 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 197 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  11 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   19 nodes to be scored   (111 eliminated genes)
## 
##   Level 8:   24 nodes to be scored   (855 eliminated genes)
## 
##   Level 7:   27 nodes to be scored   (2264 eliminated genes)
## 
##   Level 6:   34 nodes to be scored   (4832 eliminated genes)
## 
##   Level 5:   31 nodes to be scored   (6330 eliminated genes)
## 
##   Level 4:   21 nodes to be scored   (8237 eliminated genes)
## 
##   Level 3:   24 nodes to be scored   (9238 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (9586 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9689 eliminated genes)
## [1] "Significant CC terms for bisque module: 12"
## 
## Building most specific GOs .....
##  ( 1654 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1851 GO terms and 3123 relations. )
## 
## Annotating nodes ...............
##  ( 9746 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 236 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  7 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   21 nodes to be scored   (0 eliminated genes)
## 
##   Level 8:   33 nodes to be scored   (682 eliminated genes)
## 
##   Level 7:   43 nodes to be scored   (2248 eliminated genes)
## 
##   Level 6:   40 nodes to be scored   (5327 eliminated genes)
## 
##   Level 5:   39 nodes to be scored   (6725 eliminated genes)
## 
##   Level 4:   23 nodes to be scored   (8280 eliminated genes)
## 
##   Level 3:   27 nodes to be scored   (9258 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (9595 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9700 eliminated genes)
## [1] "Significant CC terms for chocolate module: 12"
## 
## Building most specific GOs .....
##  ( 1654 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1851 GO terms and 3123 relations. )
## 
## Annotating nodes ...............
##  ( 9746 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 284 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  21 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   28 nodes to be scored   (181 eliminated genes)
## 
##   Level 8:   39 nodes to be scored   (1276 eliminated genes)
## 
##   Level 7:   44 nodes to be scored   (2688 eliminated genes)
## 
##   Level 6:   45 nodes to be scored   (5405 eliminated genes)
## 
##   Level 5:   44 nodes to be scored   (6747 eliminated genes)
## 
##   Level 4:   25 nodes to be scored   (8298 eliminated genes)
## 
##   Level 3:   30 nodes to be scored   (9282 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (9605 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9700 eliminated genes)
## [1] "Significant CC terms for darkgrey module: 12"
## 
## Building most specific GOs .....
##  ( 1654 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1851 GO terms and 3123 relations. )
## 
## Annotating nodes ...............
##  ( 9746 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 321 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 12:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 11:  7 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  25 nodes to be scored   (15 eliminated genes)
## 
##   Level 9:   38 nodes to be scored   (240 eliminated genes)
## 
##   Level 8:   49 nodes to be scored   (1207 eliminated genes)
## 
##   Level 7:   45 nodes to be scored   (2699 eliminated genes)
## 
##   Level 6:   47 nodes to be scored   (5317 eliminated genes)
## 
##   Level 5:   46 nodes to be scored   (6789 eliminated genes)
## 
##   Level 4:   28 nodes to be scored   (8322 eliminated genes)
## 
##   Level 3:   32 nodes to be scored   (9272 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (9605 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9700 eliminated genes)
## [1] "Significant CC terms for darkred module: 12"
## 
## Building most specific GOs .....
##  ( 1654 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1851 GO terms and 3123 relations. )
## 
## Annotating nodes ...............
##  ( 9746 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 268 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  16 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   31 nodes to be scored   (71 eliminated genes)
## 
##   Level 8:   38 nodes to be scored   (1116 eliminated genes)
## 
##   Level 7:   36 nodes to be scored   (2563 eliminated genes)
## 
##   Level 6:   46 nodes to be scored   (5211 eliminated genes)
## 
##   Level 5:   46 nodes to be scored   (6457 eliminated genes)
## 
##   Level 4:   24 nodes to be scored   (8276 eliminated genes)
## 
##   Level 3:   26 nodes to be scored   (9270 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (9604 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9698 eliminated genes)
## [1] "Significant CC terms for darksalmon module: 12"
## 
## Building most specific GOs .....
##  ( 1654 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1851 GO terms and 3123 relations. )
## 
## Annotating nodes ...............
##  ( 9746 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 255 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  6 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  16 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   22 nodes to be scored   (239 eliminated genes)
## 
##   Level 8:   33 nodes to be scored   (1128 eliminated genes)
## 
##   Level 7:   40 nodes to be scored   (2208 eliminated genes)
## 
##   Level 6:   44 nodes to be scored   (5039 eliminated genes)
## 
##   Level 5:   42 nodes to be scored   (6663 eliminated genes)
## 
##   Level 4:   23 nodes to be scored   (8273 eliminated genes)
## 
##   Level 3:   26 nodes to be scored   (9248 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (9588 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9688 eliminated genes)
## [1] "Significant CC terms for firebrick module: 12"
## 
## Building most specific GOs .....
##  ( 1654 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1851 GO terms and 3123 relations. )
## 
## Annotating nodes ...............
##  ( 9746 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 295 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  12 nodes to be scored   (0 eliminated genes)
## 
##   Level 10:  28 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   40 nodes to be scored   (335 eliminated genes)
## 
##   Level 8:   45 nodes to be scored   (1502 eliminated genes)
## 
##   Level 7:   42 nodes to be scored   (2924 eliminated genes)
## 
##   Level 6:   37 nodes to be scored   (5334 eliminated genes)
## 
##   Level 5:   34 nodes to be scored   (6705 eliminated genes)
## 
##   Level 4:   28 nodes to be scored   (8161 eliminated genes)
## 
##   Level 3:   26 nodes to be scored   (9185 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (9575 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9700 eliminated genes)
## [1] "Significant CC terms for gainsboro module: 22"
## 
## Building most specific GOs .....
##  ( 1654 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1851 GO terms and 3123 relations. )
## 
## Annotating nodes ...............
##  ( 9746 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 339 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 12:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 11:  7 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  29 nodes to be scored   (29 eliminated genes)
## 
##   Level 9:   40 nodes to be scored   (253 eliminated genes)
## 
##   Level 8:   47 nodes to be scored   (1490 eliminated genes)
## 
##   Level 7:   48 nodes to be scored   (2744 eliminated genes)
## 
##   Level 6:   55 nodes to be scored   (5295 eliminated genes)
## 
##   Level 5:   52 nodes to be scored   (6767 eliminated genes)
## 
##   Level 4:   29 nodes to be scored   (8334 eliminated genes)
## 
##   Level 3:   28 nodes to be scored   (9287 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (9606 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9700 eliminated genes)
## [1] "Significant CC terms for lightcoral module: 27"
## 
## Building most specific GOs .....
##  ( 1654 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1851 GO terms and 3123 relations. )
## 
## Annotating nodes ...............
##  ( 9746 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 332 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 12:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 11:  9 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  24 nodes to be scored   (29 eliminated genes)
## 
##   Level 9:   38 nodes to be scored   (362 eliminated genes)
## 
##   Level 8:   43 nodes to be scored   (1423 eliminated genes)
## 
##   Level 7:   53 nodes to be scored   (2958 eliminated genes)
## 
##   Level 6:   53 nodes to be scored   (5532 eliminated genes)
## 
##   Level 5:   51 nodes to be scored   (6922 eliminated genes)
## 
##   Level 4:   29 nodes to be scored   (8299 eliminated genes)
## 
##   Level 3:   28 nodes to be scored   (9287 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (9606 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9700 eliminated genes)
## [1] "Significant CC terms for lightsalmon module: 12"
## 
## Building most specific GOs .....
##  ( 1654 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1851 GO terms and 3123 relations. )
## 
## Annotating nodes ...............
##  ( 9746 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 339 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  11 nodes to be scored   (0 eliminated genes)
## 
##   Level 10:  36 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   48 nodes to be scored   (433 eliminated genes)
## 
##   Level 8:   44 nodes to be scored   (1615 eliminated genes)
## 
##   Level 7:   48 nodes to be scored   (3107 eliminated genes)
## 
##   Level 6:   50 nodes to be scored   (5480 eliminated genes)
## 
##   Level 5:   42 nodes to be scored   (6857 eliminated genes)
## 
##   Level 4:   31 nodes to be scored   (8290 eliminated genes)
## 
##   Level 3:   26 nodes to be scored   (9251 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (9596 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9700 eliminated genes)
## [1] "Significant CC terms for maroon module: 20"
## 
## Building most specific GOs .....
##  ( 1654 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1851 GO terms and 3123 relations. )
## 
## Annotating nodes ...............
##  ( 9746 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 284 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 12:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 11:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  22 nodes to be scored   (15 eliminated genes)
## 
##   Level 9:   39 nodes to be scored   (174 eliminated genes)
## 
##   Level 8:   43 nodes to be scored   (1296 eliminated genes)
## 
##   Level 7:   39 nodes to be scored   (2655 eliminated genes)
## 
##   Level 6:   42 nodes to be scored   (5192 eliminated genes)
## 
##   Level 5:   37 nodes to be scored   (6624 eliminated genes)
## 
##   Level 4:   25 nodes to be scored   (8201 eliminated genes)
## 
##   Level 3:   28 nodes to be scored   (9194 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (9574 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9700 eliminated genes)
## [1] "Significant CC terms for orangered module: 12"
## 
## Building most specific GOs .....
##  ( 1654 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1851 GO terms and 3123 relations. )
## 
## Annotating nodes ...............
##  ( 9746 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 335 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 12:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 11:  12 nodes to be scored   (0 eliminated genes)
## 
##   Level 10:  32 nodes to be scored   (15 eliminated genes)
## 
##   Level 9:   43 nodes to be scored   (389 eliminated genes)
## 
##   Level 8:   47 nodes to be scored   (1570 eliminated genes)
## 
##   Level 7:   44 nodes to be scored   (2935 eliminated genes)
## 
##   Level 6:   47 nodes to be scored   (5444 eliminated genes)
## 
##   Level 5:   44 nodes to be scored   (6750 eliminated genes)
## 
##   Level 4:   35 nodes to be scored   (7973 eliminated genes)
## 
##   Level 3:   27 nodes to be scored   (9193 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (9575 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9700 eliminated genes)
## [1] "Significant CC terms for peru module: 12"
## 
## Building most specific GOs .....
##  ( 1654 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1851 GO terms and 3123 relations. )
## 
## Annotating nodes ...............
##  ( 9746 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 56 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   2 nodes to be scored    (23 eliminated genes)
## 
##   Level 8:   3 nodes to be scored    (23 eliminated genes)
## 
##   Level 7:   6 nodes to be scored    (70 eliminated genes)
## 
##   Level 6:   7 nodes to be scored    (2475 eliminated genes)
## 
##   Level 5:   14 nodes to be scored   (3691 eliminated genes)
## 
##   Level 4:   11 nodes to be scored   (6303 eliminated genes)
## 
##   Level 3:   9 nodes to be scored    (9171 eliminated genes)
## 
##   Level 2:   1 nodes to be scored    (9577 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9673 eliminated genes)
## [1] "Significant CC terms for red module: 12"
## 
## Building most specific GOs .....
##  ( 1654 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1851 GO terms and 3123 relations. )
## 
## Annotating nodes ...............
##  ( 9746 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 348 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  6 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  27 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   46 nodes to be scored   (275 eliminated genes)
## 
##   Level 8:   53 nodes to be scored   (1415 eliminated genes)
## 
##   Level 7:   49 nodes to be scored   (3062 eliminated genes)
## 
##   Level 6:   54 nodes to be scored   (5484 eliminated genes)
## 
##   Level 5:   48 nodes to be scored   (6838 eliminated genes)
## 
##   Level 4:   32 nodes to be scored   (8322 eliminated genes)
## 
##   Level 3:   30 nodes to be scored   (9268 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (9606 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (9700 eliminated genes)
## [1] "Significant CC terms for snow module: 12"

for(i in 1:length(modules)){
  if (!all(is.na(ResCC[[i]]$ResSel))) {
    Plot <- topGOBarplot(ResCC[[i]]$ResSel, terms=12, pvalTh=0.01, title=modules[i], palette=NULL)
    GOPlots$CC_Bar[[i]] <- Plot
    names(GOPlots$CC_Bar)[i] <- modules[i]
    }else{
      cat(modules[i], " module has no significant selected terms")
      next}
}

do.call(grid.arrange, c(GOPlots$CC_Bar, ncol = 3))

5. Gene Ontology Analysis - edc progenitors

GeneVectors <- buildGeneVector(paths$EDCs_Progenitors)
modules <- names(GeneVectors)

5.1 Biological Process

ResBP <- list()

for(i in 1:length(modules)){
  paste("Module: ", modules[i])
  BPann <- topGO::annFUN.org(whichOnto="BP", feasibleGenes=names(GeneVectors[[modules[i]]]), mapping="org.Hs.eg.db", ID="symbol") %>% topGO::inverseList()

  Res <- topGOResults(Genes=GeneVectors[[modules[i]]], gene2GO=BPann, ontology='BP',
                      description=NULL, nodeSize=15, algorithm='weight01',
                      statistic='fisher', EnTh=2, PvalTh=0.01, minTerms=12)
  print(paste('Significant BP terms for', modules[i], 'module:', dim(Res$ResSel)[1]))
  ResBP[[i]] <- Res
  names(ResBP)[i] <- modules[i]
  #write.table(Res$ResSel, file=paste0(OutputFolder, modules[i], '_BP.txt'), sep='\t', row.names=FALSE)
}
## 
## Building most specific GOs .....
##  ( 7183 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 10977 GO terms and 24566 relations. )
## 
## Annotating nodes ...............
##  ( 3190 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1619 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  4 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  10 nodes to be scored   (18 eliminated genes)
## 
##   Level 13:  14 nodes to be scored   (87 eliminated genes)
## 
##   Level 12:  27 nodes to be scored   (229 eliminated genes)
## 
##   Level 11:  51 nodes to be scored   (667 eliminated genes)
## 
##   Level 10:  87 nodes to be scored   (1054 eliminated genes)
## 
##   Level 9:   163 nodes to be scored  (1320 eliminated genes)
## 
##   Level 8:   224 nodes to be scored  (1657 eliminated genes)
## 
##   Level 7:   286 nodes to be scored  (2116 eliminated genes)
## 
##   Level 6:   310 nodes to be scored  (2564 eliminated genes)
## 
##   Level 5:   232 nodes to be scored  (2811 eliminated genes)
## 
##   Level 4:   127 nodes to be scored  (3047 eliminated genes)
## 
##   Level 3:   65 nodes to be scored   (3118 eliminated genes)
## 
##   Level 2:   17 nodes to be scored   (3141 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3154 eliminated genes)
## [1] "Significant BP terms for brown module: 12"
## 
## Building most specific GOs .....
##  ( 7183 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 10977 GO terms and 24566 relations. )
## 
## Annotating nodes ...............
##  ( 3190 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1996 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  10 nodes to be scored   (33 eliminated genes)
## 
##   Level 13:  26 nodes to be scored   (94 eliminated genes)
## 
##   Level 12:  40 nodes to be scored   (222 eliminated genes)
## 
##   Level 11:  79 nodes to be scored   (762 eliminated genes)
## 
##   Level 10:  139 nodes to be scored  (1123 eliminated genes)
## 
##   Level 9:   223 nodes to be scored  (1419 eliminated genes)
## 
##   Level 8:   276 nodes to be scored  (1770 eliminated genes)
## 
##   Level 7:   351 nodes to be scored  (2220 eliminated genes)
## 
##   Level 6:   349 nodes to be scored  (2616 eliminated genes)
## 
##   Level 5:   259 nodes to be scored  (2855 eliminated genes)
## 
##   Level 4:   149 nodes to be scored  (3060 eliminated genes)
## 
##   Level 3:   71 nodes to be scored   (3119 eliminated genes)
## 
##   Level 2:   16 nodes to be scored   (3142 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3155 eliminated genes)
## [1] "Significant BP terms for coral module: 18"
## 
## Building most specific GOs .....
##  ( 7183 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 10977 GO terms and 24566 relations. )
## 
## Annotating nodes ...............
##  ( 3190 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 612 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  1 nodes to be scored    (15 eliminated genes)
## 
##   Level 13:  4 nodes to be scored    (27 eliminated genes)
## 
##   Level 12:  9 nodes to be scored    (36 eliminated genes)
## 
##   Level 11:  20 nodes to be scored   (444 eliminated genes)
## 
##   Level 10:  34 nodes to be scored   (688 eliminated genes)
## 
##   Level 9:   56 nodes to be scored   (904 eliminated genes)
## 
##   Level 8:   64 nodes to be scored   (1205 eliminated genes)
## 
##   Level 7:   92 nodes to be scored   (1518 eliminated genes)
## 
##   Level 6:   103 nodes to be scored  (1985 eliminated genes)
## 
##   Level 5:   104 nodes to be scored  (2435 eliminated genes)
## 
##   Level 4:   69 nodes to be scored   (2869 eliminated genes)
## 
##   Level 3:   41 nodes to be scored   (3079 eliminated genes)
## 
##   Level 2:   12 nodes to be scored   (3120 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3137 eliminated genes)
## [1] "Significant BP terms for darkgrey module: 12"
## 
## Building most specific GOs .....
##  ( 7183 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 10977 GO terms and 24566 relations. )
## 
## Annotating nodes ...............
##  ( 3190 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1202 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  4 nodes to be scored    (15 eliminated genes)
## 
##   Level 13:  10 nodes to be scored   (68 eliminated genes)
## 
##   Level 12:  16 nodes to be scored   (118 eliminated genes)
## 
##   Level 11:  32 nodes to be scored   (621 eliminated genes)
## 
##   Level 10:  53 nodes to be scored   (961 eliminated genes)
## 
##   Level 9:   113 nodes to be scored  (1156 eliminated genes)
## 
##   Level 8:   145 nodes to be scored  (1472 eliminated genes)
## 
##   Level 7:   215 nodes to be scored  (1909 eliminated genes)
## 
##   Level 6:   232 nodes to be scored  (2368 eliminated genes)
## 
##   Level 5:   200 nodes to be scored  (2744 eliminated genes)
## 
##   Level 4:   110 nodes to be scored  (3025 eliminated genes)
## 
##   Level 3:   51 nodes to be scored   (3110 eliminated genes)
## 
##   Level 2:   16 nodes to be scored   (3139 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3153 eliminated genes)
## [1] "Significant BP terms for darkred module: 12"
## 
## Building most specific GOs .....
##  ( 7183 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 10977 GO terms and 24566 relations. )
## 
## Annotating nodes ...............
##  ( 3190 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1008 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  3 nodes to be scored    (18 eliminated genes)
## 
##   Level 13:  13 nodes to be scored   (46 eliminated genes)
## 
##   Level 12:  21 nodes to be scored   (85 eliminated genes)
## 
##   Level 11:  32 nodes to be scored   (655 eliminated genes)
## 
##   Level 10:  56 nodes to be scored   (993 eliminated genes)
## 
##   Level 9:   86 nodes to be scored   (1176 eliminated genes)
## 
##   Level 8:   114 nodes to be scored  (1416 eliminated genes)
## 
##   Level 7:   161 nodes to be scored  (1809 eliminated genes)
## 
##   Level 6:   194 nodes to be scored  (2177 eliminated genes)
## 
##   Level 5:   168 nodes to be scored  (2574 eliminated genes)
## 
##   Level 4:   95 nodes to be scored   (2936 eliminated genes)
## 
##   Level 3:   47 nodes to be scored   (3099 eliminated genes)
## 
##   Level 2:   14 nodes to be scored   (3131 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3144 eliminated genes)
## [1] "Significant BP terms for gainsboro module: 12"
## 
## Building most specific GOs .....
##  ( 7183 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 10977 GO terms and 24566 relations. )
## 
## Annotating nodes ...............
##  ( 3190 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 325 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 14:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 13:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 12:  5 nodes to be scored    (76 eliminated genes)
## 
##   Level 11:  8 nodes to be scored    (426 eliminated genes)
## 
##   Level 10:  13 nodes to be scored   (785 eliminated genes)
## 
##   Level 9:   29 nodes to be scored   (912 eliminated genes)
## 
##   Level 8:   33 nodes to be scored   (1043 eliminated genes)
## 
##   Level 7:   47 nodes to be scored   (1309 eliminated genes)
## 
##   Level 6:   54 nodes to be scored   (1573 eliminated genes)
## 
##   Level 5:   55 nodes to be scored   (1968 eliminated genes)
## 
##   Level 4:   40 nodes to be scored   (2610 eliminated genes)
## 
##   Level 3:   26 nodes to be scored   (2949 eliminated genes)
## 
##   Level 2:   10 nodes to be scored   (3104 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3136 eliminated genes)
## [1] "Significant BP terms for goldenrod module: 12"
## 
## Building most specific GOs .....
##  ( 7183 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 10977 GO terms and 24566 relations. )
## 
## Annotating nodes ...............
##  ( 3190 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1873 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  4 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  8 nodes to be scored    (18 eliminated genes)
## 
##   Level 13:  22 nodes to be scored   (70 eliminated genes)
## 
##   Level 12:  37 nodes to be scored   (200 eliminated genes)
## 
##   Level 11:  59 nodes to be scored   (744 eliminated genes)
## 
##   Level 10:  115 nodes to be scored  (1070 eliminated genes)
## 
##   Level 9:   189 nodes to be scored  (1307 eliminated genes)
## 
##   Level 8:   259 nodes to be scored  (1678 eliminated genes)
## 
##   Level 7:   345 nodes to be scored  (2187 eliminated genes)
## 
##   Level 6:   342 nodes to be scored  (2570 eliminated genes)
## 
##   Level 5:   260 nodes to be scored  (2846 eliminated genes)
## 
##   Level 4:   145 nodes to be scored  (3055 eliminated genes)
## 
##   Level 3:   69 nodes to be scored   (3118 eliminated genes)
## 
##   Level 2:   17 nodes to be scored   (3142 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3155 eliminated genes)
## [1] "Significant BP terms for maroon module: 15"
## 
## Building most specific GOs .....
##  ( 7183 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 10977 GO terms and 24566 relations. )
## 
## Annotating nodes ...............
##  ( 3190 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 0 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## Warning in getSigGroups(object, test.stat): No enrichment can pe performed -
## there are no feasible GO terms!
## [1] "Significant BP terms for orange module: 12"
## 
## Building most specific GOs .....
##  ( 7183 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 10977 GO terms and 24566 relations. )
## 
## Annotating nodes ...............
##  ( 3190 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1755 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  8 nodes to be scored    (33 eliminated genes)
## 
##   Level 13:  18 nodes to be scored   (72 eliminated genes)
## 
##   Level 12:  25 nodes to be scored   (207 eliminated genes)
## 
##   Level 11:  51 nodes to be scored   (699 eliminated genes)
## 
##   Level 10:  104 nodes to be scored  (1028 eliminated genes)
## 
##   Level 9:   189 nodes to be scored  (1335 eliminated genes)
## 
##   Level 8:   252 nodes to be scored  (1717 eliminated genes)
## 
##   Level 7:   324 nodes to be scored  (2206 eliminated genes)
## 
##   Level 6:   318 nodes to be scored  (2591 eliminated genes)
## 
##   Level 5:   247 nodes to be scored  (2823 eliminated genes)
## 
##   Level 4:   135 nodes to be scored  (3036 eliminated genes)
## 
##   Level 3:   63 nodes to be scored   (3114 eliminated genes)
## 
##   Level 2:   15 nodes to be scored   (3139 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3154 eliminated genes)
## [1] "Significant BP terms for peachpuff module: 12"
## 
## Building most specific GOs .....
##  ( 7183 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 10977 GO terms and 24566 relations. )
## 
## Annotating nodes ...............
##  ( 3190 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1084 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 14:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 13:  12 nodes to be scored   (0 eliminated genes)
## 
##   Level 12:  15 nodes to be scored   (129 eliminated genes)
## 
##   Level 11:  26 nodes to be scored   (614 eliminated genes)
## 
##   Level 10:  55 nodes to be scored   (927 eliminated genes)
## 
##   Level 9:   100 nodes to be scored  (1135 eliminated genes)
## 
##   Level 8:   137 nodes to be scored  (1432 eliminated genes)
## 
##   Level 7:   180 nodes to be scored  (1869 eliminated genes)
## 
##   Level 6:   203 nodes to be scored  (2327 eliminated genes)
## 
##   Level 5:   178 nodes to be scored  (2709 eliminated genes)
## 
##   Level 4:   105 nodes to be scored  (3000 eliminated genes)
## 
##   Level 3:   54 nodes to be scored   (3099 eliminated genes)
## 
##   Level 2:   15 nodes to be scored   (3137 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3154 eliminated genes)
## [1] "Significant BP terms for snow module: 12"

GOPlots <- list()

for(i in 1:length(modules)){
  if (!all(is.na(ResBP[[i]]$ResSel))) {
    Plot <- topGOBarplot(ResBP[[i]]$ResSel, terms=12, pvalTh=0.01, title=modules[i], palette=NULL)
    GOPlots$BP_Bar[[i]] <- Plot
    names(GOPlots$BP_Bar)[i] <- modules[i]
    }else{
      cat(modules[i], " module has no significant selected terms")
      next}
}
## orange  module has no significant selected terms

do.call(grid.arrange, c(GOPlots$BP_Bar, ncol = 3))

5.2 Molecular Function

ResMF <- list()

for(i in 1:length(modules)){
  MFann <- topGO::annFUN.org(whichOnto="MF", feasibleGenes=names(GeneVectors[[modules[i]]]), mapping="org.Hs.eg.db", ID="symbol") %>% topGO::inverseList()
  Res <- topGOResults(Genes=GeneVectors[[modules[i]]], gene2GO=MFann, ontology='MF',
                      description=NULL, nodeSize=15, algorithm='weight01',
                      statistic='fisher', EnTh=2, PvalTh=0.01, minTerms=12)
  print(paste('Significant MF terms for', modules[i], 'module:', dim(Res$ResSel)[1]))
  ResMF[[i]] <- Res
  names(ResMF)[i] <- modules[i]
  #write.table(Res$ResSel, file=paste0(OutputFolder, modules[i], '_MF.txt'), sep='\t', row.names=FALSE)
}
## 
## Building most specific GOs .....
##  ( 2078 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 2592 GO terms and 3378 relations. )
## 
## Annotating nodes ...............
##  ( 3228 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 213 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   7 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   11 nodes to be scored   (233 eliminated genes)
## 
##   Level 7:   16 nodes to be scored   (736 eliminated genes)
## 
##   Level 6:   36 nodes to be scored   (836 eliminated genes)
## 
##   Level 5:   50 nodes to be scored   (997 eliminated genes)
## 
##   Level 4:   54 nodes to be scored   (1760 eliminated genes)
## 
##   Level 3:   27 nodes to be scored   (2375 eliminated genes)
## 
##   Level 2:   10 nodes to be scored   (2719 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3177 eliminated genes)
## [1] "Significant MF terms for brown module: 12"
## 
## Building most specific GOs .....
##  ( 2078 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 2592 GO terms and 3378 relations. )
## 
## Annotating nodes ...............
##  ( 3228 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 235 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   3 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   9 nodes to be scored    (233 eliminated genes)
## 
##   Level 7:   16 nodes to be scored   (620 eliminated genes)
## 
##   Level 6:   41 nodes to be scored   (767 eliminated genes)
## 
##   Level 5:   60 nodes to be scored   (1066 eliminated genes)
## 
##   Level 4:   62 nodes to be scored   (1800 eliminated genes)
## 
##   Level 3:   31 nodes to be scored   (2377 eliminated genes)
## 
##   Level 2:   11 nodes to be scored   (2748 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3192 eliminated genes)
## [1] "Significant MF terms for coral module: 12"
## 
## Building most specific GOs .....
##  ( 2078 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 2592 GO terms and 3378 relations. )
## 
## Annotating nodes ...............
##  ( 3228 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 112 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 9:   2 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   3 nodes to be scored    (0 eliminated genes)
## 
##   Level 7:   8 nodes to be scored    (393 eliminated genes)
## 
##   Level 6:   15 nodes to be scored   (704 eliminated genes)
## 
##   Level 5:   22 nodes to be scored   (751 eliminated genes)
## 
##   Level 4:   31 nodes to be scored   (1239 eliminated genes)
## 
##   Level 3:   22 nodes to be scored   (1855 eliminated genes)
## 
##   Level 2:   8 nodes to be scored    (2476 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3143 eliminated genes)
## [1] "Significant MF terms for darkgrey module: 12"
## 
## Building most specific GOs .....
##  ( 2078 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 2592 GO terms and 3378 relations. )
## 
## Annotating nodes ...............
##  ( 3228 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 168 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   5 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   8 nodes to be scored    (233 eliminated genes)
## 
##   Level 7:   14 nodes to be scored   (674 eliminated genes)
## 
##   Level 6:   27 nodes to be scored   (775 eliminated genes)
## 
##   Level 5:   38 nodes to be scored   (921 eliminated genes)
## 
##   Level 4:   39 nodes to be scored   (1553 eliminated genes)
## 
##   Level 3:   26 nodes to be scored   (2287 eliminated genes)
## 
##   Level 2:   9 nodes to be scored    (2611 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3184 eliminated genes)
## [1] "Significant MF terms for darkred module: 12"
## 
## Building most specific GOs .....
##  ( 2078 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 2592 GO terms and 3378 relations. )
## 
## Annotating nodes ...............
##  ( 3228 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 123 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   3 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   5 nodes to be scored    (233 eliminated genes)
## 
##   Level 7:   9 nodes to be scored    (340 eliminated genes)
## 
##   Level 6:   20 nodes to be scored   (418 eliminated genes)
## 
##   Level 5:   30 nodes to be scored   (906 eliminated genes)
## 
##   Level 4:   30 nodes to be scored   (1320 eliminated genes)
## 
##   Level 3:   19 nodes to be scored   (2114 eliminated genes)
## 
##   Level 2:   5 nodes to be scored    (2427 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3136 eliminated genes)
## [1] "Significant MF terms for gainsboro module: 12"
## 
## Building most specific GOs .....
##  ( 2078 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 2592 GO terms and 3378 relations. )
## 
## Annotating nodes ...............
##  ( 3228 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 69 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   3 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   3 nodes to be scored    (233 eliminated genes)
## 
##   Level 7:   5 nodes to be scored    (620 eliminated genes)
## 
##   Level 6:   9 nodes to be scored    (659 eliminated genes)
## 
##   Level 5:   14 nodes to be scored   (720 eliminated genes)
## 
##   Level 4:   14 nodes to be scored   (824 eliminated genes)
## 
##   Level 3:   14 nodes to be scored   (1105 eliminated genes)
## 
##   Level 2:   5 nodes to be scored    (1666 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3070 eliminated genes)
## [1] "Significant MF terms for goldenrod module: 12"
## 
## Building most specific GOs .....
##  ( 2078 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 2592 GO terms and 3378 relations. )
## 
## Annotating nodes ...............
##  ( 3228 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 247 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   9 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   13 nodes to be scored   (253 eliminated genes)
## 
##   Level 7:   20 nodes to be scored   (750 eliminated genes)
## 
##   Level 6:   35 nodes to be scored   (846 eliminated genes)
## 
##   Level 5:   63 nodes to be scored   (1059 eliminated genes)
## 
##   Level 4:   60 nodes to be scored   (1779 eliminated genes)
## 
##   Level 3:   33 nodes to be scored   (2475 eliminated genes)
## 
##   Level 2:   11 nodes to be scored   (2706 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3189 eliminated genes)
## [1] "Significant MF terms for maroon module: 12"
## 
## Building most specific GOs .....
##  ( 2078 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 2592 GO terms and 3378 relations. )
## 
## Annotating nodes ...............
##  ( 3228 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 0 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## Warning in getSigGroups(object, test.stat): No enrichment can pe performed -
## there are no feasible GO terms!
## [1] "Significant MF terms for orange module: 12"
## 
## Building most specific GOs .....
##  ( 2078 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 2592 GO terms and 3378 relations. )
## 
## Annotating nodes ...............
##  ( 3228 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 249 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   6 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   9 nodes to be scored    (253 eliminated genes)
## 
##   Level 7:   21 nodes to be scored   (707 eliminated genes)
## 
##   Level 6:   37 nodes to be scored   (787 eliminated genes)
## 
##   Level 5:   63 nodes to be scored   (1073 eliminated genes)
## 
##   Level 4:   66 nodes to be scored   (1777 eliminated genes)
## 
##   Level 3:   32 nodes to be scored   (2419 eliminated genes)
## 
##   Level 2:   12 nodes to be scored   (2714 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3192 eliminated genes)
## [1] "Significant MF terms for peachpuff module: 12"
## 
## Building most specific GOs .....
##  ( 2078 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 2592 GO terms and 3378 relations. )
## 
## Annotating nodes ...............
##  ( 3228 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 179 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   8 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   12 nodes to be scored   (253 eliminated genes)
## 
##   Level 7:   16 nodes to be scored   (744 eliminated genes)
## 
##   Level 6:   24 nodes to be scored   (853 eliminated genes)
## 
##   Level 5:   33 nodes to be scored   (1011 eliminated genes)
## 
##   Level 4:   42 nodes to be scored   (1579 eliminated genes)
## 
##   Level 3:   31 nodes to be scored   (2159 eliminated genes)
## 
##   Level 2:   10 nodes to be scored   (2674 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3192 eliminated genes)
## [1] "Significant MF terms for snow module: 12"

for(i in 1:length(modules)){
  if (!all(is.na(ResMF[[i]]$ResSel))) {
    Plot <- topGOBarplot(ResMF[[i]]$ResSel, terms=12, pvalTh=0.01, title=modules[i], palette=NULL)
    GOPlots$MF_Bar[[i]] <- Plot
    names(GOPlots$MF_Bar)[i] <- modules[i]
    }else{
      cat(modules[i], " module has no significant selected terms")
      next}
}
## orange  module has no significant selected terms

do.call(grid.arrange, c(GOPlots$MF_Bar, ncol = 3))

5.3 Cellular Component

ResCC <- list()

for(i in 1:length(modules)){
  CCann <- topGO::annFUN.org(whichOnto="CC", feasibleGenes=names(GeneVectors[[modules[i]]]), mapping="org.Hs.eg.db", ID="symbol") %>% topGO::inverseList()
  Res <- topGOResults(Genes=GeneVectors[[modules[i]]], gene2GO=CCann, ontology='CC',
                      description=NULL, nodeSize=15, algorithm='weight01',
                      statistic='fisher', EnTh=2, PvalTh=0.01, minTerms=12)
  print(paste('Significant CC terms for', modules[i], 'module:', dim(Res$ResSel)[1]))
  ResCC[[i]] <- Res
  names(ResCC)[i] <- modules[i]
  #write.table(Res$ResSel, file=paste0(OutputFolder, modules[i], '_CC-.txt'), sep='\t', row.names=FALSE)
}
## 
## Building most specific GOs .....
##  ( 1160 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1418 GO terms and 2399 relations. )
## 
## Annotating nodes ...............
##  ( 3321 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 245 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  13 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   24 nodes to be scored   (0 eliminated genes)
## 
##   Level 8:   34 nodes to be scored   (370 eliminated genes)
## 
##   Level 7:   36 nodes to be scored   (822 eliminated genes)
## 
##   Level 6:   43 nodes to be scored   (1758 eliminated genes)
## 
##   Level 5:   42 nodes to be scored   (2170 eliminated genes)
## 
##   Level 4:   23 nodes to be scored   (2818 eliminated genes)
## 
##   Level 3:   27 nodes to be scored   (3150 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (3268 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3308 eliminated genes)
## [1] "Significant CC terms for brown module: 12"
## 
## Building most specific GOs .....
##  ( 1160 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1418 GO terms and 2399 relations. )
## 
## Annotating nodes ...............
##  ( 3321 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 300 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  16 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   36 nodes to be scored   (71 eliminated genes)
## 
##   Level 8:   46 nodes to be scored   (453 eliminated genes)
## 
##   Level 7:   48 nodes to be scored   (951 eliminated genes)
## 
##   Level 6:   47 nodes to be scored   (1864 eliminated genes)
## 
##   Level 5:   44 nodes to be scored   (2264 eliminated genes)
## 
##   Level 4:   27 nodes to be scored   (2823 eliminated genes)
## 
##   Level 3:   30 nodes to be scored   (3151 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (3270 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3308 eliminated genes)
## [1] "Significant CC terms for coral module: 12"
## 
## Building most specific GOs .....
##  ( 1160 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1418 GO terms and 2399 relations. )
## 
## Annotating nodes ...............
##  ( 3321 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 121 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   9 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   16 nodes to be scored   (23 eliminated genes)
## 
##   Level 7:   20 nodes to be scored   (449 eliminated genes)
## 
##   Level 6:   21 nodes to be scored   (1551 eliminated genes)
## 
##   Level 5:   18 nodes to be scored   (1957 eliminated genes)
## 
##   Level 4:   15 nodes to be scored   (2654 eliminated genes)
## 
##   Level 3:   18 nodes to be scored   (3108 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (3209 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3244 eliminated genes)
## [1] "Significant CC terms for darkgrey module: 12"
## 
## Building most specific GOs .....
##  ( 1160 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1418 GO terms and 2399 relations. )
## 
## Annotating nodes ...............
##  ( 3321 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 175 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   10 nodes to be scored   (0 eliminated genes)
## 
##   Level 8:   20 nodes to be scored   (157 eliminated genes)
## 
##   Level 7:   29 nodes to be scored   (502 eliminated genes)
## 
##   Level 6:   33 nodes to be scored   (1697 eliminated genes)
## 
##   Level 5:   34 nodes to be scored   (2190 eliminated genes)
## 
##   Level 4:   22 nodes to be scored   (2803 eliminated genes)
## 
##   Level 3:   21 nodes to be scored   (3142 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (3268 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3304 eliminated genes)
## [1] "Significant CC terms for darkred module: 12"
## 
## Building most specific GOs .....
##  ( 1160 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1418 GO terms and 2399 relations. )
## 
## Annotating nodes ...............
##  ( 3321 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 120 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   12 nodes to be scored   (0 eliminated genes)
## 
##   Level 8:   16 nodes to be scored   (205 eliminated genes)
## 
##   Level 7:   18 nodes to be scored   (576 eliminated genes)
## 
##   Level 6:   14 nodes to be scored   (1540 eliminated genes)
## 
##   Level 5:   16 nodes to be scored   (2052 eliminated genes)
## 
##   Level 4:   17 nodes to be scored   (2539 eliminated genes)
## 
##   Level 3:   19 nodes to be scored   (3090 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (3259 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3308 eliminated genes)
## [1] "Significant CC terms for gainsboro module: 12"
## 
## Building most specific GOs .....
##  ( 1160 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1418 GO terms and 2399 relations. )
## 
## Annotating nodes ...............
##  ( 3321 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 52 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 9:   1 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   4 nodes to be scored    (0 eliminated genes)
## 
##   Level 7:   6 nodes to be scored    (38 eliminated genes)
## 
##   Level 6:   7 nodes to be scored    (1019 eliminated genes)
## 
##   Level 5:   10 nodes to be scored   (1355 eliminated genes)
## 
##   Level 4:   11 nodes to be scored   (2319 eliminated genes)
## 
##   Level 3:   10 nodes to be scored   (2966 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (3252 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3293 eliminated genes)
## [1] "Significant CC terms for goldenrod module: 12"
## 
## Building most specific GOs .....
##  ( 1160 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1418 GO terms and 2399 relations. )
## 
## Annotating nodes ...............
##  ( 3321 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 291 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  19 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   33 nodes to be scored   (66 eliminated genes)
## 
##   Level 8:   42 nodes to be scored   (463 eliminated genes)
## 
##   Level 7:   48 nodes to be scored   (924 eliminated genes)
## 
##   Level 6:   48 nodes to be scored   (1839 eliminated genes)
## 
##   Level 5:   43 nodes to be scored   (2300 eliminated genes)
## 
##   Level 4:   25 nodes to be scored   (2826 eliminated genes)
## 
##   Level 3:   27 nodes to be scored   (3151 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (3268 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3308 eliminated genes)
## [1] "Significant CC terms for maroon module: 12"
## 
## Building most specific GOs .....
##  ( 1160 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1418 GO terms and 2399 relations. )
## 
## Annotating nodes ...............
##  ( 3321 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 0 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## Warning in getSigGroups(object, test.stat): No enrichment can pe performed -
## there are no feasible GO terms!
## [1] "Significant CC terms for orange module: 12"
## 
## Building most specific GOs .....
##  ( 1160 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1418 GO terms and 2399 relations. )
## 
## Annotating nodes ...............
##  ( 3321 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 286 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  18 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   33 nodes to be scored   (103 eliminated genes)
## 
##   Level 8:   44 nodes to be scored   (321 eliminated genes)
## 
##   Level 7:   47 nodes to be scored   (910 eliminated genes)
## 
##   Level 6:   44 nodes to be scored   (1862 eliminated genes)
## 
##   Level 5:   42 nodes to be scored   (2269 eliminated genes)
## 
##   Level 4:   23 nodes to be scored   (2823 eliminated genes)
## 
##   Level 3:   27 nodes to be scored   (3149 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (3268 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3308 eliminated genes)
## [1] "Significant CC terms for peachpuff module: 12"
## 
## Building most specific GOs .....
##  ( 1160 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1418 GO terms and 2399 relations. )
## 
## Annotating nodes ...............
##  ( 3321 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 176 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  6 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   14 nodes to be scored   (48 eliminated genes)
## 
##   Level 8:   19 nodes to be scored   (128 eliminated genes)
## 
##   Level 7:   26 nodes to be scored   (386 eliminated genes)
## 
##   Level 6:   33 nodes to be scored   (1506 eliminated genes)
## 
##   Level 5:   34 nodes to be scored   (2070 eliminated genes)
## 
##   Level 4:   19 nodes to be scored   (2798 eliminated genes)
## 
##   Level 3:   20 nodes to be scored   (3139 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (3268 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (3304 eliminated genes)
## [1] "Significant CC terms for snow module: 12"

for(i in 1:length(modules)){
  if (!all(is.na(ResCC[[i]]$ResSel))) {
    Plot <- topGOBarplot(ResCC[[i]]$ResSel, terms=12, pvalTh=0.01, title=modules[i], palette=NULL)
    GOPlots$CC_Bar[[i]] <- Plot
    names(GOPlots$CC_Bar)[i] <- modules[i]
    }else{
      cat(modules[i], " module has no significant selected terms")
      next}
}
## orange  module has no significant selected terms

do.call(grid.arrange, c(GOPlots$CC_Bar, ncol = 3))

6. Gene Ontology Analysis - edc neurons

GeneVectors <- buildGeneVector(paths$EDCs_Neurons)
modules <- names(GeneVectors)

6.1 Biological Process

ResBP <- list()

for(i in 1:length(modules)){
  BPann <- topGO::annFUN.org(whichOnto="BP", feasibleGenes=names(GeneVectors[[modules[i]]]), mapping="org.Hs.eg.db", ID="symbol") %>% topGO::inverseList()

  Res <- topGOResults(Genes=GeneVectors[[modules[i]]], gene2GO=BPann, ontology='BP',
                      description=NULL, nodeSize=15, algorithm='weight01',
                      statistic='fisher', EnTh=2, PvalTh=0.01, minTerms=12)
  print(paste('Significant BP terms for', modules[i], 'module:', dim(Res$ResSel)[1]))
  ResBP[[i]] <- Res
  names(ResBP)[i] <- modules[i]
  #write.table(Res$ResSel, file=paste0(OutputFolder, modules[i], '_BP.txt'), sep='\t', row.names=FALSE)
}
## 
## Building most specific GOs .....
##  ( 8797 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 12582 GO terms and 28336 relations. )
## 
## Annotating nodes ...............
##  ( 5780 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 2236 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  4 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  7 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  13 nodes to be scored   (54 eliminated genes)
## 
##   Level 13:  26 nodes to be scored   (126 eliminated genes)
## 
##   Level 12:  46 nodes to be scored   (349 eliminated genes)
## 
##   Level 11:  87 nodes to be scored   (1226 eliminated genes)
## 
##   Level 10:  174 nodes to be scored  (1828 eliminated genes)
## 
##   Level 9:   280 nodes to be scored  (2416 eliminated genes)
## 
##   Level 8:   323 nodes to be scored  (3125 eliminated genes)
## 
##   Level 7:   383 nodes to be scored  (4128 eliminated genes)
## 
##   Level 6:   376 nodes to be scored  (4842 eliminated genes)
## 
##   Level 5:   273 nodes to be scored  (5257 eliminated genes)
## 
##   Level 4:   152 nodes to be scored  (5534 eliminated genes)
## 
##   Level 3:   74 nodes to be scored   (5639 eliminated genes)
## 
##   Level 2:   17 nodes to be scored   (5698 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5721 eliminated genes)
## [1] "Significant BP terms for darkgrey module: 24"
## 
## Building most specific GOs .....
##  ( 8797 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 12582 GO terms and 28336 relations. )
## 
## Annotating nodes ...............
##  ( 5780 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1860 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  6 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  15 nodes to be scored   (19 eliminated genes)
## 
##   Level 13:  27 nodes to be scored   (138 eliminated genes)
## 
##   Level 12:  43 nodes to be scored   (418 eliminated genes)
## 
##   Level 11:  70 nodes to be scored   (1243 eliminated genes)
## 
##   Level 10:  136 nodes to be scored  (1908 eliminated genes)
## 
##   Level 9:   218 nodes to be scored  (2378 eliminated genes)
## 
##   Level 8:   263 nodes to be scored  (3145 eliminated genes)
## 
##   Level 7:   308 nodes to be scored  (3914 eliminated genes)
## 
##   Level 6:   310 nodes to be scored  (4746 eliminated genes)
## 
##   Level 5:   241 nodes to be scored  (5202 eliminated genes)
## 
##   Level 4:   142 nodes to be scored  (5516 eliminated genes)
## 
##   Level 3:   64 nodes to be scored   (5636 eliminated genes)
## 
##   Level 2:   15 nodes to be scored   (5702 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5722 eliminated genes)
## [1] "Significant BP terms for darksalmon module: 20"
## 
## Building most specific GOs .....
##  ( 8797 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 12582 GO terms and 28336 relations. )
## 
## Annotating nodes ...............
##  ( 5780 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1345 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  4 nodes to be scored    (15 eliminated genes)
## 
##   Level 13:  12 nodes to be scored   (15 eliminated genes)
## 
##   Level 12:  25 nodes to be scored   (201 eliminated genes)
## 
##   Level 11:  43 nodes to be scored   (1006 eliminated genes)
## 
##   Level 10:  75 nodes to be scored   (1696 eliminated genes)
## 
##   Level 9:   140 nodes to be scored  (2092 eliminated genes)
## 
##   Level 8:   177 nodes to be scored  (2827 eliminated genes)
## 
##   Level 7:   228 nodes to be scored  (3760 eliminated genes)
## 
##   Level 6:   244 nodes to be scored  (4542 eliminated genes)
## 
##   Level 5:   202 nodes to be scored  (5114 eliminated genes)
## 
##   Level 4:   114 nodes to be scored  (5498 eliminated genes)
## 
##   Level 3:   61 nodes to be scored   (5629 eliminated genes)
## 
##   Level 2:   17 nodes to be scored   (5694 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5721 eliminated genes)
## [1] "Significant BP terms for gainsboro module: 12"
## 
## Building most specific GOs .....
##  ( 8797 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 12582 GO terms and 28336 relations. )
## 
## Annotating nodes ...............
##  ( 5780 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1440 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  5 nodes to be scored    (24 eliminated genes)
## 
##   Level 13:  16 nodes to be scored   (31 eliminated genes)
## 
##   Level 12:  27 nodes to be scored   (226 eliminated genes)
## 
##   Level 11:  51 nodes to be scored   (1137 eliminated genes)
## 
##   Level 10:  95 nodes to be scored   (1800 eliminated genes)
## 
##   Level 9:   155 nodes to be scored  (2284 eliminated genes)
## 
##   Level 8:   193 nodes to be scored  (3040 eliminated genes)
## 
##   Level 7:   239 nodes to be scored  (3860 eliminated genes)
## 
##   Level 6:   245 nodes to be scored  (4574 eliminated genes)
## 
##   Level 5:   211 nodes to be scored  (5136 eliminated genes)
## 
##   Level 4:   123 nodes to be scored  (5501 eliminated genes)
## 
##   Level 3:   61 nodes to be scored   (5634 eliminated genes)
## 
##   Level 2:   14 nodes to be scored   (5698 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5725 eliminated genes)
## [1] "Significant BP terms for mistyrose module: 12"
## 
## Building most specific GOs .....
##  ( 8797 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 12582 GO terms and 28336 relations. )
## 
## Annotating nodes ...............
##  ( 5780 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 631 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 14:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 13:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 12:  8 nodes to be scored    (90 eliminated genes)
## 
##   Level 11:  13 nodes to be scored   (753 eliminated genes)
## 
##   Level 10:  30 nodes to be scored   (1200 eliminated genes)
## 
##   Level 9:   45 nodes to be scored   (1332 eliminated genes)
## 
##   Level 8:   64 nodes to be scored   (1821 eliminated genes)
## 
##   Level 7:   99 nodes to be scored   (2433 eliminated genes)
## 
##   Level 6:   121 nodes to be scored  (3301 eliminated genes)
## 
##   Level 5:   116 nodes to be scored  (4164 eliminated genes)
## 
##   Level 4:   75 nodes to be scored   (4970 eliminated genes)
## 
##   Level 3:   40 nodes to be scored   (5557 eliminated genes)
## 
##   Level 2:   12 nodes to be scored   (5651 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5713 eliminated genes)
## [1] "Significant BP terms for peachpuff module: 12"
## 
## Building most specific GOs .....
##  ( 8797 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 12582 GO terms and 28336 relations. )
## 
## Annotating nodes ...............
##  ( 5780 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1010 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 14:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 13:  13 nodes to be scored   (0 eliminated genes)
## 
##   Level 12:  24 nodes to be scored   (197 eliminated genes)
## 
##   Level 11:  36 nodes to be scored   (902 eliminated genes)
## 
##   Level 10:  60 nodes to be scored   (1532 eliminated genes)
## 
##   Level 9:   92 nodes to be scored   (1994 eliminated genes)
## 
##   Level 8:   108 nodes to be scored  (2622 eliminated genes)
## 
##   Level 7:   165 nodes to be scored  (3165 eliminated genes)
## 
##   Level 6:   178 nodes to be scored  (3965 eliminated genes)
## 
##   Level 5:   164 nodes to be scored  (4767 eliminated genes)
## 
##   Level 4:   96 nodes to be scored   (5378 eliminated genes)
## 
##   Level 3:   55 nodes to be scored   (5619 eliminated genes)
## 
##   Level 2:   13 nodes to be scored   (5692 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5725 eliminated genes)
## [1] "Significant BP terms for saddlebrown module: 12"
## 
## Building most specific GOs .....
##  ( 8797 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 12582 GO terms and 28336 relations. )
## 
## Annotating nodes ...............
##  ( 5780 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 1912 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  14 nodes to be scored   (37 eliminated genes)
## 
##   Level 13:  27 nodes to be scored   (75 eliminated genes)
## 
##   Level 12:  39 nodes to be scored   (417 eliminated genes)
## 
##   Level 11:  67 nodes to be scored   (1174 eliminated genes)
## 
##   Level 10:  135 nodes to be scored  (1823 eliminated genes)
## 
##   Level 9:   204 nodes to be scored  (2274 eliminated genes)
## 
##   Level 8:   270 nodes to be scored  (3108 eliminated genes)
## 
##   Level 7:   341 nodes to be scored  (3939 eliminated genes)
## 
##   Level 6:   329 nodes to be scored  (4769 eliminated genes)
## 
##   Level 5:   247 nodes to be scored  (5224 eliminated genes)
## 
##   Level 4:   149 nodes to be scored  (5537 eliminated genes)
## 
##   Level 3:   68 nodes to be scored   (5645 eliminated genes)
## 
##   Level 2:   16 nodes to be scored   (5702 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5725 eliminated genes)
## [1] "Significant BP terms for salmon module: 12"
## 
## Building most specific GOs .....
##  ( 8797 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 12582 GO terms and 28336 relations. )
## 
## Annotating nodes ...............
##  ( 5780 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 888 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 16:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 15:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 14:  8 nodes to be scored    (18 eliminated genes)
## 
##   Level 13:  13 nodes to be scored   (104 eliminated genes)
## 
##   Level 12:  15 nodes to be scored   (229 eliminated genes)
## 
##   Level 11:  24 nodes to be scored   (492 eliminated genes)
## 
##   Level 10:  44 nodes to be scored   (1468 eliminated genes)
## 
##   Level 9:   70 nodes to be scored   (1877 eliminated genes)
## 
##   Level 8:   101 nodes to be scored  (2309 eliminated genes)
## 
##   Level 7:   142 nodes to be scored  (2878 eliminated genes)
## 
##   Level 6:   172 nodes to be scored  (3907 eliminated genes)
## 
##   Level 5:   148 nodes to be scored  (4742 eliminated genes)
## 
##   Level 4:   85 nodes to be scored   (5414 eliminated genes)
## 
##   Level 3:   45 nodes to be scored   (5597 eliminated genes)
## 
##   Level 2:   14 nodes to be scored   (5676 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5717 eliminated genes)
## [1] "Significant BP terms for silver module: 19"

GOPlots <- list()

for(i in 1:length(modules)){
  if (!all(is.na(ResBP[[i]]$ResSel))) {
    Plot <- topGOBarplot(ResBP[[i]]$ResSel, terms=12, pvalTh=0.01, title=modules[i], palette=NULL)
    GOPlots$BP_Bar[[i]] <- Plot
    names(GOPlots$BP_Bar)[i] <- modules[i]
    }else{
      cat(modules[i], " module has no significant selected terms")
      next}
}

do.call(grid.arrange, c(GOPlots$BP_Bar, ncol = 3))

6.2 Molecular Function

ResMF <- list()

for(i in 1:length(modules)){
  MFann <- topGO::annFUN.org(whichOnto="MF", feasibleGenes=names(GeneVectors[[modules[i]]]), mapping="org.Hs.eg.db", ID="symbol") %>% topGO::inverseList()
  Res <- topGOResults(Genes=GeneVectors[[modules[i]]], gene2GO=MFann, ontology='MF',
                      description=NULL, nodeSize=15, algorithm='weight01',
                      statistic='fisher', EnTh=2, PvalTh=0.01, minTerms=12)
  print(paste('Significant MF terms for', modules[i], 'module:', dim(Res$ResSel)[1]))
  ResMF[[i]] <- Res
  names(ResMF)[i] <- modules[i]
  #write.table(Res$ResSel, file=paste0(OutputFolder, modules[i], '_MF.txt'), sep='\t', row.names=FALSE)
}
## 
## Building most specific GOs .....
##  ( 2855 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3347 GO terms and 4399 relations. )
## 
## Annotating nodes ...............
##  ( 5907 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 314 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  5 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   11 nodes to be scored   (23 eliminated genes)
## 
##   Level 8:   19 nodes to be scored   (467 eliminated genes)
## 
##   Level 7:   29 nodes to be scored   (1291 eliminated genes)
## 
##   Level 6:   53 nodes to be scored   (1502 eliminated genes)
## 
##   Level 5:   85 nodes to be scored   (1949 eliminated genes)
## 
##   Level 4:   69 nodes to be scored   (3120 eliminated genes)
## 
##   Level 3:   30 nodes to be scored   (4415 eliminated genes)
## 
##   Level 2:   11 nodes to be scored   (4900 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5817 eliminated genes)
## [1] "Significant MF terms for darkgrey module: 12"
## 
## Building most specific GOs .....
##  ( 2855 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3347 GO terms and 4399 relations. )
## 
## Annotating nodes ...............
##  ( 5907 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 273 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   7 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   6 nodes to be scored    (378 eliminated genes)
## 
##   Level 7:   21 nodes to be scored   (1146 eliminated genes)
## 
##   Level 6:   47 nodes to be scored   (1244 eliminated genes)
## 
##   Level 5:   68 nodes to be scored   (1908 eliminated genes)
## 
##   Level 4:   71 nodes to be scored   (3084 eliminated genes)
## 
##   Level 3:   37 nodes to be scored   (4229 eliminated genes)
## 
##   Level 2:   14 nodes to be scored   (4758 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5840 eliminated genes)
## [1] "Significant MF terms for darksalmon module: 12"
## 
## Building most specific GOs .....
##  ( 2855 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3347 GO terms and 4399 relations. )
## 
## Annotating nodes ...............
##  ( 5907 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 249 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   11 nodes to be scored   (15 eliminated genes)
## 
##   Level 8:   11 nodes to be scored   (437 eliminated genes)
## 
##   Level 7:   21 nodes to be scored   (1244 eliminated genes)
## 
##   Level 6:   39 nodes to be scored   (1391 eliminated genes)
## 
##   Level 5:   63 nodes to be scored   (1614 eliminated genes)
## 
##   Level 4:   59 nodes to be scored   (3014 eliminated genes)
## 
##   Level 3:   30 nodes to be scored   (4245 eliminated genes)
## 
##   Level 2:   10 nodes to be scored   (4710 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5833 eliminated genes)
## [1] "Significant MF terms for gainsboro module: 12"
## 
## Building most specific GOs .....
##  ( 2855 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3347 GO terms and 4399 relations. )
## 
## Annotating nodes ...............
##  ( 5907 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 239 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   7 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   12 nodes to be scored   (398 eliminated genes)
## 
##   Level 7:   23 nodes to be scored   (1187 eliminated genes)
## 
##   Level 6:   43 nodes to be scored   (1434 eliminated genes)
## 
##   Level 5:   55 nodes to be scored   (1945 eliminated genes)
## 
##   Level 4:   55 nodes to be scored   (2971 eliminated genes)
## 
##   Level 3:   28 nodes to be scored   (3913 eliminated genes)
## 
##   Level 2:   13 nodes to be scored   (4728 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5831 eliminated genes)
## [1] "Significant MF terms for mistyrose module: 12"
## 
## Building most specific GOs .....
##  ( 2855 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3347 GO terms and 4399 relations. )
## 
## Annotating nodes ...............
##  ( 5907 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 57 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 8:   1 nodes to be scored    (0 eliminated genes)
## 
##   Level 7:   2 nodes to be scored    (0 eliminated genes)
## 
##   Level 6:   7 nodes to be scored    (482 eliminated genes)
## 
##   Level 5:   14 nodes to be scored   (672 eliminated genes)
## 
##   Level 4:   15 nodes to be scored   (1007 eliminated genes)
## 
##   Level 3:   12 nodes to be scored   (2568 eliminated genes)
## 
##   Level 2:   5 nodes to be scored    (3868 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5666 eliminated genes)
## [1] "Significant MF terms for peachpuff module: 12"
## 
## Building most specific GOs .....
##  ( 2855 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3347 GO terms and 4399 relations. )
## 
## Annotating nodes ...............
##  ( 5907 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 203 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   5 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   9 nodes to be scored    (378 eliminated genes)
## 
##   Level 7:   16 nodes to be scored   (1145 eliminated genes)
## 
##   Level 6:   35 nodes to be scored   (1337 eliminated genes)
## 
##   Level 5:   44 nodes to be scored   (1681 eliminated genes)
## 
##   Level 4:   50 nodes to be scored   (2442 eliminated genes)
## 
##   Level 3:   30 nodes to be scored   (3798 eliminated genes)
## 
##   Level 2:   12 nodes to be scored   (4594 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5789 eliminated genes)
## [1] "Significant MF terms for saddlebrown module: 12"
## 
## Building most specific GOs .....
##  ( 2855 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3347 GO terms and 4399 relations. )
## 
## Annotating nodes ...............
##  ( 5907 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 298 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   6 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   12 nodes to be scored   (378 eliminated genes)
## 
##   Level 7:   26 nodes to be scored   (1161 eliminated genes)
## 
##   Level 6:   55 nodes to be scored   (1380 eliminated genes)
## 
##   Level 5:   73 nodes to be scored   (1858 eliminated genes)
## 
##   Level 4:   75 nodes to be scored   (3211 eliminated genes)
## 
##   Level 3:   36 nodes to be scored   (4400 eliminated genes)
## 
##   Level 2:   13 nodes to be scored   (4897 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5829 eliminated genes)
## [1] "Significant MF terms for salmon module: 12"
## 
## Building most specific GOs .....
##  ( 2855 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 3347 GO terms and 4399 relations. )
## 
## Annotating nodes ...............
##  ( 5907 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 129 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 9:   1 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   4 nodes to be scored    (0 eliminated genes)
## 
##   Level 7:   10 nodes to be scored   (566 eliminated genes)
## 
##   Level 6:   19 nodes to be scored   (739 eliminated genes)
## 
##   Level 5:   29 nodes to be scored   (990 eliminated genes)
## 
##   Level 4:   35 nodes to be scored   (2203 eliminated genes)
## 
##   Level 3:   22 nodes to be scored   (3906 eliminated genes)
## 
##   Level 2:   8 nodes to be scored    (4635 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (5820 eliminated genes)
## [1] "Significant MF terms for silver module: 12"

for(i in 1:length(modules)){
  if (!all(is.na(ResMF[[i]]$ResSel))) {
    Plot <- topGOBarplot(ResMF[[i]]$ResSel, terms=12, pvalTh=0.01, title=modules[i], palette=NULL)
    GOPlots$MF_Bar[[i]] <- Plot
    names(GOPlots$MF_Bar)[i] <- modules[i]
    }else{
      cat(modules[i], " module has no significant selected terms")
      next}
}

do.call(grid.arrange, c(GOPlots$MF_Bar, ncol = 3))

6.3 Cellular Component

ResCC <- list()

for(i in 1:length(modules)){
  CCann <- topGO::annFUN.org(whichOnto="CC", feasibleGenes=names(GeneVectors[[modules[i]]]), mapping="org.Hs.eg.db", ID="symbol") %>% topGO::inverseList()
  Res <- topGOResults(Genes=GeneVectors[[modules[i]]], gene2GO=CCann, ontology='CC',
                      description=NULL, nodeSize=15, algorithm='weight01',
                      statistic='fisher', EnTh=2, PvalTh=0.01, minTerms=12)
  print(paste('Significant CC terms for', modules[i], 'module:', dim(Res$ResSel)[1]))
  ResCC[[i]] <- Res
  names(ResCC)[i] <- modules[i]
  #write.table(Res$ResSel, file=paste0(OutputFolder, modules[i], '_CC-.txt'), sep='\t', row.names=FALSE)
}
## 
## Building most specific GOs .....
##  ( 1444 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1670 GO terms and 2839 relations. )
## 
## Annotating nodes ...............
##  ( 6044 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 323 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  23 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   38 nodes to be scored   (102 eliminated genes)
## 
##   Level 8:   48 nodes to be scored   (1003 eliminated genes)
## 
##   Level 7:   49 nodes to be scored   (1798 eliminated genes)
## 
##   Level 6:   53 nodes to be scored   (3603 eliminated genes)
## 
##   Level 5:   49 nodes to be scored   (4354 eliminated genes)
## 
##   Level 4:   27 nodes to be scored   (5243 eliminated genes)
## 
##   Level 3:   30 nodes to be scored   (5775 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (5964 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6009 eliminated genes)
## [1] "Significant CC terms for darkgrey module: 12"
## 
## Building most specific GOs .....
##  ( 1444 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1670 GO terms and 2839 relations. )
## 
## Annotating nodes ...............
##  ( 6044 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 362 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  11 nodes to be scored   (0 eliminated genes)
## 
##   Level 10:  31 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   44 nodes to be scored   (311 eliminated genes)
## 
##   Level 8:   56 nodes to be scored   (1018 eliminated genes)
## 
##   Level 7:   52 nodes to be scored   (1969 eliminated genes)
## 
##   Level 6:   55 nodes to be scored   (3618 eliminated genes)
## 
##   Level 5:   45 nodes to be scored   (4334 eliminated genes)
## 
##   Level 4:   34 nodes to be scored   (5209 eliminated genes)
## 
##   Level 3:   31 nodes to be scored   (5744 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (5954 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6016 eliminated genes)
## [1] "Significant CC terms for darksalmon module: 17"
## 
## Building most specific GOs .....
##  ( 1444 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1670 GO terms and 2839 relations. )
## 
## Annotating nodes ...............
##  ( 6044 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 286 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 12:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 11:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  19 nodes to be scored   (23 eliminated genes)
## 
##   Level 9:   35 nodes to be scored   (81 eliminated genes)
## 
##   Level 8:   45 nodes to be scored   (829 eliminated genes)
## 
##   Level 7:   44 nodes to be scored   (1911 eliminated genes)
## 
##   Level 6:   43 nodes to be scored   (3643 eliminated genes)
## 
##   Level 5:   42 nodes to be scored   (4321 eliminated genes)
## 
##   Level 4:   23 nodes to be scored   (5220 eliminated genes)
## 
##   Level 3:   29 nodes to be scored   (5776 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (5966 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6016 eliminated genes)
## [1] "Significant CC terms for gainsboro module: 12"
## 
## Building most specific GOs .....
##  ( 1444 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1670 GO terms and 2839 relations. )
## 
## Annotating nodes ...............
##  ( 6044 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 317 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  7 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  26 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   40 nodes to be scored   (182 eliminated genes)
## 
##   Level 8:   44 nodes to be scored   (1052 eliminated genes)
## 
##   Level 7:   46 nodes to be scored   (1952 eliminated genes)
## 
##   Level 6:   46 nodes to be scored   (3533 eliminated genes)
## 
##   Level 5:   45 nodes to be scored   (4259 eliminated genes)
## 
##   Level 4:   32 nodes to be scored   (5223 eliminated genes)
## 
##   Level 3:   28 nodes to be scored   (5765 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (5964 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6015 eliminated genes)
## [1] "Significant CC terms for mistyrose module: 12"
## 
## Building most specific GOs .....
##  ( 1444 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1670 GO terms and 2839 relations. )
## 
## Annotating nodes ...............
##  ( 6044 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 97 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 10:  2 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   6 nodes to be scored    (0 eliminated genes)
## 
##   Level 8:   8 nodes to be scored    (103 eliminated genes)
## 
##   Level 7:   13 nodes to be scored   (443 eliminated genes)
## 
##   Level 6:   15 nodes to be scored   (2417 eliminated genes)
## 
##   Level 5:   19 nodes to be scored   (3144 eliminated genes)
## 
##   Level 4:   17 nodes to be scored   (4682 eliminated genes)
## 
##   Level 3:   14 nodes to be scored   (5697 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (5947 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6009 eliminated genes)
## [1] "Significant CC terms for peachpuff module: 12"
## 
## Building most specific GOs .....
##  ( 1444 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1670 GO terms and 2839 relations. )
## 
## Annotating nodes ...............
##  ( 6044 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 245 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  3 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  16 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   34 nodes to be scored   (74 eliminated genes)
## 
##   Level 8:   32 nodes to be scored   (753 eliminated genes)
## 
##   Level 7:   39 nodes to be scored   (1762 eliminated genes)
## 
##   Level 6:   32 nodes to be scored   (3330 eliminated genes)
## 
##   Level 5:   34 nodes to be scored   (4207 eliminated genes)
## 
##   Level 4:   28 nodes to be scored   (5158 eliminated genes)
## 
##   Level 3:   24 nodes to be scored   (5726 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (5954 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6016 eliminated genes)
## [1] "Significant CC terms for saddlebrown module: 12"
## 
## Building most specific GOs .....
##  ( 1444 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1670 GO terms and 2839 relations. )
## 
## Annotating nodes ...............
##  ( 6044 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 308 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  4 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  22 nodes to be scored   (0 eliminated genes)
## 
##   Level 9:   39 nodes to be scored   (126 eliminated genes)
## 
##   Level 8:   43 nodes to be scored   (931 eliminated genes)
## 
##   Level 7:   48 nodes to be scored   (1917 eliminated genes)
## 
##   Level 6:   45 nodes to be scored   (3557 eliminated genes)
## 
##   Level 5:   46 nodes to be scored   (4348 eliminated genes)
## 
##   Level 4:   29 nodes to be scored   (5226 eliminated genes)
## 
##   Level 3:   29 nodes to be scored   (5768 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (5966 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6016 eliminated genes)
## [1] "Significant CC terms for salmon module: 12"
## 
## Building most specific GOs .....
##  ( 1444 GO terms found. )
## 
## Build GO DAG topology ..........
##  ( 1670 GO terms and 2839 relations. )
## 
## Annotating nodes ...............
##  ( 6044 genes annotated to the GO terms. )
## 
##           -- Weight01 Algorithm -- 
## 
##       the algorithm is scoring 195 nontrivial nodes
##       parameters: 
##           test statistic: fisher
## 
##   Level 11:  1 nodes to be scored    (0 eliminated genes)
## 
##   Level 10:  7 nodes to be scored    (0 eliminated genes)
## 
##   Level 9:   17 nodes to be scored   (30 eliminated genes)
## 
##   Level 8:   27 nodes to be scored   (253 eliminated genes)
## 
##   Level 7:   31 nodes to be scored   (717 eliminated genes)
## 
##   Level 6:   32 nodes to be scored   (3294 eliminated genes)
## 
##   Level 5:   36 nodes to be scored   (4180 eliminated genes)
## 
##   Level 4:   21 nodes to be scored   (5170 eliminated genes)
## 
##   Level 3:   20 nodes to be scored   (5768 eliminated genes)
## 
##   Level 2:   2 nodes to be scored    (5964 eliminated genes)
## 
##   Level 1:   1 nodes to be scored    (6015 eliminated genes)
## [1] "Significant CC terms for silver module: 12"

for(i in 1:length(modules)){
  if (!all(is.na(ResCC[[i]]$ResSel))) {
    Plot <- topGOBarplot(ResCC[[i]]$ResSel, terms=12, pvalTh=0.01, title=modules[i], palette=NULL)
    GOPlots$CC_Bar[[i]] <- Plot
    names(GOPlots$CC_Bar)[i] <- modules[i]
    }else{
      cat(modules[i], " module has no significant selected terms")
      next}
}

do.call(grid.arrange, c(GOPlots$CC_Bar, ncol = 3))

7. Savings

SessionInfo <- sessionInfo()
Date <- date()

Date

## [1] "Mon Jun 30 16:28:51 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 datasets  utils     methods  
## [8] base     
## 
## other attached packages:
##  [1] topGO_2.50.0                SparseM_1.81               
##  [3] GO.db_3.16.0                graph_1.76.0               
##  [5] org.Hs.eg.db_3.16.0         AnnotationDbi_1.60.0       
##  [7] SummarizedExperiment_1.28.0 Biobase_2.58.0             
##  [9] GenomicRanges_1.50.2        GenomeInfoDb_1.34.9        
## [11] IRanges_2.32.0              S4Vectors_0.36.1           
## [13] BiocGenerics_0.44.0         MatrixGenerics_1.10.0      
## [15] matrixStats_0.63.0          viridis_0.6.2              
## [17] viridisLite_0.4.1           gridExtra_2.3              
## [19] ggplot2_3.4.1               dplyr_1.1.0                
## 
## loaded via a namespace (and not attached):
##  [1] lattice_0.20-45        png_0.1-8              Biostrings_2.66.0     
##  [4] digest_0.6.31          utf8_1.2.3             R6_2.5.1              
##  [7] RSQLite_2.3.0          evaluate_0.20          highr_0.10            
## [10] httr_1.4.5             pillar_1.8.1           zlibbioc_1.44.0       
## [13] rlang_1.1.1            rstudioapi_0.14        jquerylib_0.1.4       
## [16] blob_1.2.3             Matrix_1.5-3           rmarkdown_2.20        
## [19] stringr_1.5.0          RCurl_1.98-1.10        bit_4.0.5             
## [22] munsell_0.5.0          DelayedArray_0.24.0    compiler_4.2.1        
## [25] xfun_0.37              pkgconfig_2.0.3        htmltools_0.5.4       
## [28] tidyselect_1.2.0       KEGGREST_1.38.0        tibble_3.2.1          
## [31] GenomeInfoDbData_1.2.9 fansi_1.0.4            crayon_1.5.2          
## [34] withr_2.5.0            bitops_1.0-7           grid_4.2.1            
## [37] jsonlite_1.8.4         gtable_0.3.1           lifecycle_1.0.3       
## [40] DBI_1.1.3              magrittr_2.0.3         scales_1.2.1          
## [43] stringi_1.7.12         cli_3.6.1              cachem_1.0.7          
## [46] farver_2.1.1           XVector_0.38.0         renv_0.15.4           
## [49] bslib_0.4.2            generics_0.1.3         vctrs_0.6.2           
## [52] tools_4.2.1            bit64_4.0.5            glue_1.6.2            
## [55] fastmap_1.1.1          yaml_2.3.7             colorspace_2.1-0      
## [58] BiocManager_1.30.22    memoise_2.0.1          knitr_1.42            
## [61] sass_0.4.5