Retrieve only protein coding esnsemble gene ids and gene symbols

Question

[iibrams07]

I tried without success different ways to retrieve the current list of ensemble gene ids including the gene symbol for only protein coding genes by using the R library Biomart. Here is the code:

library(biomaRt)
ensembl = useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
results <- getBM(attributes=c("ensembl_gene_id","gene_biotype"),filters = c("ensembl_gene_id","biotype"), values=list("protein_coding"), mart=ensembl)
results

The error message is:

Error in names(values) <- filters : 
'names' attribute [2] must be the same length as the vector [1]

I also need the gene symbol for each ensemble gene id (example, TSPAN6). I eventually included "hgnc_id" in both the attributes vector as well as the filters one with a similar error message as the one shown above. What should I do to accomplish the task ? Many thanks for any comment.

[iraun]

In attributes you have gene_biotype, while in filters biotype, maybe that has something to do with the error?

Answer 1

[Basti]

The error comes from the fact you specified two filters whereas you only provide one value. Additionally, "biotype" is not an attribute of listFilters(ensembl) but I guess "transcript_biotype" is what you would need.

Then to overcome your issue, you can do :

results <- getBM(attributes=c("ensembl_gene_id","hgnc_symbol","transcript_biotype"),filters = c("transcript_biotype"), values=list("protein_coding"), mart=ensembl)
results

If you need further information, have a look at listAttributes(ensembl) and select what you need

[LayneSadler]

Since most ensembl biomart attributes are either gene_* or transcript_*, I don't think it makes sense to use gene_id with transcript_biotype