Lecture3_One-hundred-software-in-bioinformatics005_WeGO

Jimmy（jmzeng1314@outlook.com）

library(GOstats)

library(org.Hs.eg.db)

tmp=toTable(org.Hs.egGO)

new_tmp=unlist(tapply(tmp[,2],as.factor(tmp[,1]),function(x) paste(x,collapse =" "),simplify =F))

EG2GO=tapply(tmp[,2],as.factor(tmp[,1]),function(x) x)

GO2EG=tapply(tmp[,1],as.factor(tmp[,2]),function(x) x)

all_go_gene=names(EG2GO);

diff_gene=all_go_gene[unique(floor(runif(1000,0,18000)) + 1)]

diff_gene_go=new_tmp[diff_gene]

write.table(diff_gene_go,"diff_gene_go",quote = F,sep="\t",col.names = F)

GOES = c('BP','CC', 'MF');

annotationPKG='org.Hs.eg.db'

for (ontology in GOES) {

# perform enrichment test. locusid is DEGs

hyperG.params = new("GOHyperGParams", geneIds=diff_gene, universeGeneIds=NULL, annotation=annotationPKG,

ontology=ontology, pvalueCutoff=1, conditional = FALSE, testDirection = "over")

hyperG.results = hyperGTest(hyperG.params);

outHTMLname=paste("GO_",ontology,".enrichment.html",sep="")

htmlReport(hyperG.results, file=outHTMLname, summary.args=list("htmlLinks"=TRUE))

}