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Trying to annotate M. musculus SNPs but getting: Error in martCheck(mart)

Hi,

I'm trying to get information about some SNPs from BioMart but I'm getting and error with the mart and haven't been able to figure out how to fix it. This is what I've written:

data = read.csv("SNP_positions.csv")

snpmart = useMart("ENSEMBL_MART_SNP", dataset="mmusculus_snp")

out = getBM(attributes=c("refsnp_id","chr_name","chrom_start","chrom_strand","allele","consequence_type_tv","ensemble_gene_stable_id","ensembl_type","reg_feature_stable_id","reg_consequence_types"), filters=c("chr_name","chrom_start","chrom_end", values=data, mart=snpmart))

 Error in martCheck(mart) : 
  You must provide a valid Mart object. To create a Mart object use the function: useMart.  Check ?useMart for more information.

I can view all the attributes and filters in the mart so I know I selected what I needed, I just don't know why I'm getting this error. Any help is greatly appreciated!

r snp biomart
• 2,491 views • link
written by mm • mm

2 answers

In your getBM() function, the values and mart parameters are inside the filters parameter.

• 1 views • link
written by igor igor

Thanks for finding my mistake!

• 1 views • link
written by mm • mm

Thanks! I can't believe I missed that :)

• 0 views • link
written by mm • mm

This should have gone under @igor's answer (using "Add Comment") instead of a new answer.

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written by GenoMax GenoMax

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