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)