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'),