I have a count file containing 50 human samples. The gencode gtf file was used to map the reads. STAR was used to map and featureCounts was used to generate count data. So, the rownames in my files are ensenbl gene_ids which looks like:
"ENSG00000231251.1" "ENSG00000236335.1" "ENSG00000231949.1" "ENSG00000162510.5" total 61471. How can I convert these ids to refseq ids for edgeR analysis? I have tried several ways but failed each time.
`gids=mapIds(org.Hs.eg.db,keys = rownames(y1),keytype = 'ENSEMBL',column = "SYMBOL")` it says Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments. but the rownames are the ensembl ids!! idfound=y1$genes$genes %in% mappedkeys(org.Hs.egENSEMBL) . Only 33 match!! gids=y1$genes$genes %in% mappedkeys(org.Hs.egREFSEQ) . Only 33 match!!
y1 is the DGElist object and y$genes$genes are the ensembl ids as mentioned above. Any help in this matter? Thanks in advance. Best Regards Zillur