select_LD_variants: Select variants in LD with the index variants

In boxiangliu/vsea: Variant Set Enrichment Analysis

Description

Select variants in LD with the index variants

Usage

select_LD_variants(index_set, population, plink)

Arguments

index_set	The output from create_index_set
population	The population is one of AFR, EUR or EAS
plink	The path to plink

Details

select_LD_variants selects LD proxies for variants in the index_set based on 1000 Genomes Phase 3. The function automatically downloads 1000 Genomces Phase 3 VCF files for the specified population. The function also requires plink2 (https://www.cog-genomics.org/plink2) to perform r2 calculation.

Value

A data.table that contains the original variants in index_set, as well as their LD proxies (r2>0.7).

boxiangliu/vsea documentation built on May 20, 2019, 5:56 p.m.