根据rs号使用biomaRt做SNP注释

参考链接：biomaRt: 用R愉快检索BioMart数据库 - 简书 (jianshu.com)

1.安装biomaRt包

BiocManager::install("biomaRt")

#加载biomaRt包
library(biomaRt) 
#查看有哪些数据集
> listMarts()
               biomart                version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 107
2   ENSEMBL_MART_MOUSE      Mouse strains 107
3     ENSEMBL_MART_SNP  Ensembl Variation 107
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 107

2.选择数据库和数据集

通过函数 useMart 设置要连接的 BioMart 数据集。

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

3.从文件中读取SNP的rs号

snp_ids = read.table("SNP_list.txt",stringsAsFactors = F)[[1]]
#attributes设置需要显示的SNP信息，包括rs号，染色体号和起始位点
#获取snp的相关坐标信息
> results <- getBM(attributes = c( "refsnp_id","chr_name","chrom_start","chrom_end","allele"), 
+                  filters = "snp_filter", 
+                  values = "rs9340799", 
+                  mart = snp_mart)
#输出结果
> results
  refsnp_id chr_name chrom_start chrom_end allele
1 rs9340799        6   151842246 151842246    A/G