参考：http://www.biotrainee.com/thread-558-1-1.html
http://bioconductor.org/packages/3.7/bioc/
http://www.bioconductor.org/packages/release/bioc/html/topGO.html
topGO使用：
首先，我们制作准备文件，CC、BP、MF三个注释文件，格式为：基因ID\t GO:xxx,GO:yyy（topGO.map）
然后准备我们的差异基因列表，两列差异基因ID\t FDR。（topGO.list）
library("topGO")
geneID2GO<-readMappings(choose.files()) ##读取所有基因注释信息
geneNames<- names(geneID2GO)
data<-read.table(choose.files(), row.names = 1, header=TRUE,check.names =F) ##读取差异基因的ID
geneList<-data[,1]
names(geneList) <- rownames(data)
topDiffGenes<-function(allScore){return(allScore<0.05)}
###BP
sampleGOdata <- new("topGOdata",nodeSize = 6,ontology="BP", allGenes = geneList,annot = annFUN.gene2GO, gene2GO = geneID2GO,geneSel=topDiffGenes)
resultKS.elim <- runTest(sampleGOdata, algorithm = "elim", statistic = "ks")
allRes <- GenTable(sampleGOdata,KS = resultKS.elim,ranksOf = "classic", topNodes = attributes(resultKS.elim)$geneData[4])
write.table(allRes, file="T01_vs_T02.topGO_BP.xls", sep="\t", quote=FALSE, col.names=TRUE, row.names=FALSE)
pdf("T01_vs_T02.topGO_BP.pdf")
showSigOfNodes(sampleGOdata, score(resultKS.elim), firstSigNodes = 10, useInfo = "all")
dev.off()
png("T01_vs_T02.topGO_BP.png")
showSigOfNodes(sampleGOdata, score(resultKS.elim), firstSigNodes = 10, useInfo = "all")
dev.off()
##MF
sampleGOdata <- new("topGOdata",nodeSize = 6,ontology="MF", allGenes = geneList, annot = annFUN.gene2GO, gene2GO = geneID2GO,geneSel=topDiffGenes)
resultKS.elim <- runTest(sampleGOdata, algorithm = "elim", statistic = "ks")
allRes <- GenTable(sampleGOdata,KS = resultKS.elim,ranksOf = "classic", topNodes = attributes(resultKS.elim)$geneData[4])
write.table(allRes, file="T01_vs_T02.topGO_MF.xls", sep="\t", quote=FALSE, col.names=TRUE, row.names=FALSE)
pdf("T01_vs_T02.topGO_MF.pdf")
showSigOfNodes(sampleGOdata, score(resultKS.elim), firstSigNodes = 10, useInfo = "all")
dev.off()
png("T01_vs_T02.topGO_MF.png")
showSigOfNodes(sampleGOdata, score(resultKS.elim), firstSigNodes = 10, useInfo = "all")
dev.off()
##CC
sampleGOdata <- new("topGOdata",nodeSize = 6,ontology="CC", allGenes = geneList, annot = annFUN.gene2GO, gene2GO = geneID2GO,geneSel=topDiffGenes)
resultKS.elim <- runTest(sampleGOdata, algorithm = "elim", statistic = "ks")
allRes <- GenTable(sampleGOdata,KS = resultKS.elim,ranksOf = "classic", topNodes = attributes(resultKS.elim)$geneData[4])
write.table(allRes, file="T01_vs_T02.topGO_CC.xls", sep="\t", quote=FALSE, col.names=TRUE, row.names=FALSE)
pdf("T01_vs_T02.topGO_CC.pdf")
showSigOfNodes(sampleGOdata, score(resultKS.elim), firstSigNodes = 10, useInfo = "all")
dev.off()
png("T01_vs_T02.topGO_CC.png")
showSigOfNodes(sampleGOdata, score(resultKS.elim), firstSigNodes = 10, useInfo = "all")
dev.off()
原文地址：https://www.cnblogs.com/renping/p/9502514.html