Hi. I have a data frame of ensembl gene IDs and their corresponding canonical transcript IDs. Below is a small subset of this data frame:
geneID transcriptID ENSG00000186092 ENST00000335137 ENSG00000187634 ENST00000420190 ENSG00000187642 ENST00000341290 ENSG00000188157 ENST00000379370 ENSG00000186891 ENST00000379265
I would like to retrieve the protein coding sequences for these genes using the R package biomaRt. Using the code below I can do this:
mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") seq = getSequence(id = "ENSG00000186092", type = c("ensembl_gene_id"), seqType = "coding", mart = mart)
My issue is that I would like to add a second filter of transcript ID so that I am only getting the gene sequence for the specific transcript. However, I am not sure how to do this for the getSequence function. I have tried to add a value argument (as with getBM) but this gives the unused argument error message. Does anyone know how to do this?