将SNP ID映射到基因组坐标

Question

我有几个SNP ID(即rs16828074,rs17232800等),我想在UCSC基因组网站的Hg19基因组中找到它们的坐标.

我更愿意用它R来实现这个目标.怎么做？

Answer 1

这是使用Bioconductor包的解决方案biomaRt.它是以前发布的代码的略微更正和重新格式化的版本.

library(biomaRt) # biomaRt_2.30.0

snp_mart = useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp")

snp_ids = c("rs16828074", "rs17232800")
snp_attributes = c("refsnp_id", "chr_name", "chrom_start")

snp_locations = getBM(attributes=snp_attributes, filters="snp_filter", 
                      values=snp_ids, mart=snp_mart)

snp_locations
#    refsnp_id chr_name chrom_start
# 1 rs16828074        2   232318754
# 2 rs17232800       18    66292259

鼓励用户阅读全面的biomaRt 小插图并尝试以下biomaRt功能:

listFilters(snp_mart)
listAttributes(snp_mart)
attributePages(snp_mart)
listDatasets(snp_mart)
listMarts()