I have reads counted with rna.fa.gz from:
It's labeled with IDs that look like this:
I've extracted the REFSEQs, and used org.Mm.eg.db to get the SYMBOLs.
1 gi|126352347|ref|NM_028260.2| Immp1l
2 gi|142348699|ref|NM_010886.2| Ndufa4
Unfortunately, a number of REFSEQs seem to be obsolete.
> select(org.Mm.eg.db, keys="XM_001478046", keytype="REFSEQ", columns="SYMBOL")
Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for 'REFSEQ'. Please use the keys method to see a listing of valid arguments.
NCBI Reference Sequence: XM_001478046.1 (click to see this obsolete version)
- This sequence has been replaced by NM_001142441.
How do I use Bioconductor to convert XM_001478046 to NM_001142441(and then Sap18b)?