Gene enrichment analysis - How to get the gene names in Entrez id's?
0
0
Entering edit mode
3.5 years ago
bionewbie • 0

I am trying to perform GO analysis and I would like to derive the gene names that are associated with upregulation for log fold change of 1 and above. I am right now getting BP id, value, count, term etc. but I need the gene name as well. Also I am trying to do Kegg pathway analysis similarly and get the gene names in that as well. GO Enrichment analysis using GOstats

library(GO.db)

library(GOstats)

selectedGenes = unique(resSig[resSig$log2FoldChange>1,'entrez'])  # upregulated genes

universeGenes =  unique( mapIds(org.Hs.eg.db,
                     keys= res$ensembl,
                     column="ENTREZID",
                     keytype="ENSEMBL", #Out ID is ENSMBL
                     multiVals="first")
                    )


 hgCutoff <- 0.001

params <- new("GOHyperGParams",
     geneIds=selectedGenes,
     universeGeneIds=universeGenes,
     annotation="org.Hs.eg.db",
     ontology="BP",
     pvalueCutoff=hgCutoff,
     conditional=FALSE,
     testDirection="over")

hgOver <- hyperGTest(params)
summary(hgOver)
Bioconductor Geneenrichment RNAseq genomics • 651 views
ADD COMMENT

Login before adding your answer.

Traffic: 1062 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6