convert_gtex_to_rsids: Convert GTEx IDs to rsid

In MCorentin/vargen: Fetching Variants Related to Phenotypes Using Public Databases

Convert GTEx IDs to rsid

Description

GTEx IDs are in the format "chr_pos_ref_alt_build". To make it consistent with the rest of the package, we are converting them to rsids. We us the "gtex_lookup" which is a data.frame created by reading the gtex lookup file. (see: get_gtex_variants)

Usage

convert_gtex_to_rsids(gtex_variants, gtex_lookup_file, verbose = FALSE)

Arguments

gtex_variants	a data.frame of gtex variants obtained during "get_gtex_variants" should contain at least one column with the gtex_id as "chr_pos_alt_ref_build"
gtex_lookup_file	the lookup file, GTEx to rsids. "GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_838Indiv_Analysis_Freeze.lookup_table.txt.gz" Can be obtained using vargen_install.
verbose	if true, will print information about the conversion (default: FALSE)

Value

a vector of rsids (as some gtex ids do not have a corresponding rsid the output can be smalled than the input)

MCorentin/vargen documentation built on Feb. 6, 2024, 2:32 p.m.