I'm trying to do pathway analysis for DE porcine genes generated using DESeq2.
(A) I used package "clusterprofiler" to convert gene symbols to enterzids using the following code:
gg = bitr(m1, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Ss.eg.db") geneSS <- as.vector(gg$ENTREZID)
(B) Then I implemented 'enrichPathway' function to obtain enriched pathways. The following is the code I used, but it failed to generate the enriched pathways.
rpa <- enrichPathway(gene=geneSS, pvalueCutoff=0.05, readable=T, organism="pig") head(as.data.frame(rpa))  ID Description GeneRatio BgRatio pvalue p.adjust  qvalue Count <0 rows> (or 0-length row.names)
I was able to get a list of KEGG pathways using "erichKEGG". But, I couldn't do the same with ReactomePA. Can anyone help solve this? Thanks in advance.