get_rsid_from_position: Get rsid name from position

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

Description

This method accesses the NCI's API and queries a position (CHR & POS) and variant (REF & ALT) to obtain a rsid. If it fails, it will attempt to swap REF and ALT before giving up.

Usage

get_rsid_from_position(chrom, pos, ref, alt, assembly = valid_references)

Arguments

chrom	The name of the contig for the SNP
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")

Value

an rsid identifier of the position provided

Examples

get_rsid_from_position("9", 125711603,	"C",	"A") # "rs10760259"
get_rsid_from_position("9", 136155000, "T", "C") # "rs635634"
get_rsid_from_position("9", 136155000, "C", "T") # "rs635634"

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