Question: biomaRt: Extracting data for a particular isoform (R/bioconductor)
0
gravatar for bsmith030465
3.5 years ago by
bsmith030465100
United States
bsmith030465100 wrote:

Hi,

I was trying to extract the 5' UTR and 3'UTR coordinates for a particular isoform. My code is:

==================

library(biomaRt)

mart = useMart("ensembl")

getBM(attributes = c("5_utr_start","5_utr_end","3_utr_start","3_utr_end"),filters = "hgnc_symbol",value = "AAGAB",mart = ensembl)

==================

Is there a way that I can specify that for the gene (AAGAB), I want information for isoform 001 (ie. AAGAB-001)? Else, how do I process the data given by my query above so that I can get this information?

Or should I be doing something else altogether?

 

thanks!

 

bioconductor extract utr biomart • 1.4k views
ADD COMMENTlink modified 3.4 years ago by Biostar ♦♦ 20 • written 3.5 years ago by bsmith030465100

I suspect that specifying a query based on gene symbol is not the way to go.  You'll probably need to specify a transcript in the filter.  Do you know a transcript ID?

ADD REPLYlink written 3.5 years ago by Sean Davis25k

Thanks for the reply. So, if I want to get the details of "ENST00000538028", I should use something like:

ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")

xx <- getBM(attributes = c("5_utr_start","5_utr_end","3_utr_start","3_utr_end"),
                    filters = "ensembl_transcript_id",value = "ENST00000261880",mart = ensembl)

 

Am I using the right filters?

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by bsmith030465100

Looks right.  You might want to specify that ensembl_transcript_id in the attributes as well.

ADD REPLYlink written 3.5 years ago by Sean Davis25k

Indeed, a working example here: A: R org.Hs.eg.db matching ensembl gene ids with gene symbol

Just replace filter="ensembl_gene_id" with filter="ensembl_transcript_id"

ADD REPLYlink written 3 months ago by Kevin Blighe32k
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