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Question: Using multiple filters in BiomaRt's getSequence
0
gravatar for spiral01
2.3 years ago by
spiral01 • 100
spiral01 • 100 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 • 1.1k views
ADD COMMENT • link •
modified 2.3 years ago by Emily_Ensembl ♦ 20k • written 2.3 years ago by spiral01 • 100
1
gravatar for Emily_Ensembl
2.3 years ago by
Emily_Ensembl ♦ 20k
EMBL-EBI
Emily_Ensembl ♦ 20k 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 COMMENT • link written 2.3 years ago by Emily_Ensembl ♦ 20k

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

ADD REPLY • link written 2.3 years ago by spiral01 • 100

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

ADD REPLY • link written 2.3 years ago by Emily_Ensembl ♦ 20k
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