Thursday, October 31, 2013

biomaRt, SNP, ensembl


http://uswest.ensembl.org/info/genome/variation/index.html

http://uswest.ensembl.org/info/docs/api/variation/variation_tutorial.html
http://uswest.ensembl.org/info/docs/api/variation/variation_tutorial.html#alleles

http://uswest.ensembl.org/info/website/tutorials/Ensembl_variation_quick_reference_card.pdf

library(biomaRt)
snp.db <- useMart("snp", dataset="hsapiens_snp")
nt.biomart <- getBM(c("refsnp_id","allele","chr_name","chrom_start",                   
                      "chrom_strand","associated_gene",
                      "ensembl_gene_stable_id"),
                    filters="refsnp",
                    values=the.snps,
                    mart=snp.db)

Reference: 
http://www.biostars.org/p/1332/

Ensemble ported some dbSNP population infor about SNP
Example: rs1800944 gene CCR5
http://uswest.ensembl.org/Homo_sapiens/Phenotype/Locations?ph=763



I tried hemoglobin but did not see snps.


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