I have googled and also searched biostar but I haven't found a complete answer yet.
I am new to R and can really appreciate your help.
I want to know in my set of differentially expressed genes, what is the enrichment for Gene ontology function or pathway. I have come across other posts that mention good/popular packages in R ( Best UPDATED tool for enrichment anlysis ) but I don't know enough of R to be able to stich together the output I have from DSeq and then into the gene set enrichment package to get the list of enriched function. I use the DAVID go ontology online but would really like to learn to use it from within R.
So, this is what I have so far.
I imported the counts_table (which was measured using bedtools multicov), and used DSeq to identify differentially expressed genes. The relevant part is
res=nbinomTest(cds,"treated","untreated") FDR_THRESHOLD=0.05 resSig=res[res$padj< FDR_THRESHOLD,] namesSig=na.omit(res[res$padj<FDR_THRESHOLD,])$id
So now I have an array of enriched human genes, with names in genesymbol format, in the namesSig array.
My question: Can you please show me an example of how I can go about finding the enrichment of genes using *any* reliable gene set enrichment package in R?