10、差異基因topGO富集
參考：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，我們制作準備文件，CC、BP、MF三個註釋文件，格式為：基因ID\t GO:xxx,GO:yyy（topGO.map） 然後準備我們的差異基因列表，兩列差異基因ID\t FDR。（topGO.list）library("topGO")
geneID2GO<-readMappings(choose.files()) ##讀取所有基因註釋信息
geneNames<- names(geneID2GO)
data<-read.table(choose.files(), row.names = 1, header=TRUE,check.names =F) ##讀取差異基因的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()
10、差異基因topGO富集