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Yuan Jian
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250
@yuan-jian-2603
Last seen 8.8 years ago
Hello bioconductor experts:
now I am using GOstats package to get enriched pathway:
> paramsKEGG <- new("KEGGHyperGParams", geneIds = geneCluster,
universeGeneIds = geneUniverse, annotation =
"org.Hs.eg.db",
pvalueCutoff = 0.1, testDirection = "over")
>output <- summary(hgKEGG_Over)
I can get enriched geneSymbol as below. my question is how to
correspond these geneSymbol to the entries (enclosed by square) in
KEGG pathway figure?
>overlap_EGs <- geneCluster[geneCluster %in%
unlist(mget(output$KEGGID[1], revmap(org.Hs.egPATH),ifnotfound=NA))]
>overlap_symbols <- mget(overlap_EGs, org.Hs.egSYMBOL)
thanks
Yu
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