I used to convert RefSeq accessions to gene symbols in R using biomaRt like this:
library(biomaRt)
mart<- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
refseq <- c("NM_006945", "NM_152486", "NM_198317")
getBM(filters="refseq_dna", attributes="external_gene_id", values=refseq, mart=mart)
This used to work, but now I get this error:
Invalid filters(s): refseq_dna
Please use the function 'listFilters' to get valid filter names*
I found the filter name "refseq_mrna" which produces this error:
Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'ensemblmart64.oxRefSeqmRNA__dm' doesn't exist
What is the correct way to convert RefSeq accessions to gene symbols with biomaRt?
Thanks!