GO_topGO_geneSet: GOanalysis in R - topGO enrichment test terms

In perllb/deseqAbstraction: A set of functions to make DESeq pipes more smooth

GOanalysis in R - topGO enrichment test terms

Description

Do GO term enrichement and analysis for a list of genes

Usage

GO_topGO_geneSet(dabs = NULL, geneSet = NULL, org = "hsa",
  term = "BP", nodeSize = 5, outdir = ".")

Arguments

dabs:	deseq object
org:	only hg38 annotation currently supported, mm10 coming soon..
term:	which go term ("BP" "MF" or "CC")
geneSet:	list of genes for test
nodeSize:	Set smallest included node size (number of genes in term) in enrichment test
outdir:	name of output directory

Examples

dabs$makeDiffex
geneSet <- getSignName(x = dabs$test$Default,p=0.01)$up # get upregulated genes
GO_topGO_geneSet(org = "hsa",BP=T,MF=F,CC=F,geneSet=geneSet,outdir=currdir,nodeSize=3)

perllb/deseqAbstraction documentation built on Oct. 31, 2023, 2:13 a.m.