Question: Using multiple filters in BiomaRt's getSequence
gravatar for spiral01
19 months ago by
spiral0180 wrote:

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?

ensembl biomart R • 780 views
ADD COMMENTlink modified 19 months ago by Emily_Ensembl17k • written 19 months ago by spiral0180
gravatar for Emily_Ensembl
19 months ago by
Emily_Ensembl17k wrote:

Change your filter so that you're filtering by the Ensembl transcript ID:

seq = getSequence(id =  "ENST00000335137",
               type = c("ensembl_transcript_id"),
               seqType = "coding",
               mart = mart)
ADD COMMENTlink written 19 months ago by Emily_Ensembl17k

Hi Emily, thanks that does help. However is it actually possible to use two different filters?

ADD REPLYlink written 19 months ago by spiral0180

You can filter by multiple types of ID, but you can filter by a list of IDs, plus a biotype or something.

ADD REPLYlink written 18 months ago by Emily_Ensembl17k
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