GO_topGO_rank: GOanalysis in R - topGO enrichment test terms RANK based

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

GOanalysis in R - topGO enrichment test terms RANK based

Description

Do GO term enrichement and analysis for a list of genes

Usage

GO_topGO_rank(dabs = NULL, org = "hsa", term = "BP", nodeSize = 5,
  rank = "log2fc", sigCut = 1)

Arguments

dabs:	deseq object
org:	only hg38 annotation currently supported, mm10 coming soon..
term:	which go term ("BP" "MF" or "CC")
nodeSize:	Set smallest included node size (number of genes in term) in enrichment test
rank:	How to rank genes (either "log2fc" or "padj")
sigCut:	where to cut for sign genes. when rank="log2fc", it is the absolute log2FC. when rank="padj", it is p-adj value..

Examples

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

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