Question: output from getBM() function in biomaRt package
gravatar for k.askland
4.0 years ago by
United States
k.askland20 wrote:

I have been able to use the method suggested in response to my last post (biomaRt SNP (rs ID) -to-HGNC symbol mapping question) as an alternative means to obtaining rsID-HGNC symbol maps.  However, I would ideally like to compare several methods for obtaining gene mapping information for a large set of SNPs. One method I'd like to use is the getBM function from the biomaRt package by accessing the ensembl mart. However, while I can input a list of SNP rsIDs with their chromosomal locations (i.e., chromosome, start and end BP positions) with the script below, there does not appear to be a way to retain that information in the output file. The attributes list available for biomaRt does not appear to include rsID or marker location. I would like to know if there's a way to add the marker information to the set of attributes?

ChromLocMap <- getBM(c('hgnc_symbol','chromosome_name','start_position','end_position', 'band'), 
        filters = c('chromosome_name', 'start', 'end'),
        values=as.list(rsIDlist[,c(as.character("chr"),"startBP","endBP")]), mart=ensembl)

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