Entering edit mode
There is an error in biomart::getBM
when one of the attributes is "entrezgene_id"
.
mart <- biomaRt::useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", version = 107)
biomaRt::getBM(attributes = c("entrezgene_id"), mart = mart)
returns the following error:
Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery, :
Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'ensembl_mart_107.hsapiens_gene_ensembl__ox_entrezgene__dm' doesn't exist
The attribute in question exists:
attr <- biomaRt::listAttributes(mart)
grep("entrez", attr$name, value = TRUE)
which returns
[1] "entrezgene_trans_name" "entrezgene_description" "entrezgene_accession" "entrezgene_id"
It seems to affect only version 107. The same code for 106 and 108 works with no issues. I'm not sure if this is a problem with biomaRt of Ensembl.