get_rsid: Get rsid name from position

In richardslab/MRutils: Utility functions for preparing data for Two-Sample MR

Description

This method combines the cached and API version of get_rsid

Usage

get_rsid(
  chrom,
  pos,
  ref,
  alt,
  assembly = valid_references,
  cache_file = NULL,
  update_cache = TRUE
)

Arguments

chrom	The name of the contig for the SNP (the "chr" prefix will be ignored if present)
pos	The (1-based) position of the SNP
ref	The reference allele (only SNPs are supported)
alt	The alternate allele (only SNPs are supported)
assembly	Which reference genome to use ("hg18", "hg19", or "hg38")
cache_file	Which file to use for caching results. if NULL will not use cache
update_cache	A boolean indicating whether to update the cache results.

Value

an rsid identifier of the position provided

Examples

get_rsid("9", 125711603, "C", "A") # "rs10760259"
get_rsid("9", 136155000, "T", "C") # "rs635634"
get_rsid("9", 136155000, "C", "T") # "rs635634"
get_rsid("chr6", 32007459, "A",	"G") # "rs12525076"
get_rsid("chr6", 32007459, "G",	"A") # "rs12525076"
get_rsid("6", 32007459, "A",	"G") # "rs12525076"

richardslab/MRutils documentation built on Dec. 22, 2021, 4 p.m.