select_background_variants: Select matched background variants

In boxiangliu/vsea: Variant Set Enrichment Analysis

Description

Select matched background variants

Usage

select_background_variants(x, snpsnap, bg_size = 200)

Arguments

x	A vector of SNP IDs (format: chr:pos, e.g. 12:56115585)
snpsnap	The SNPsnap dataset returned by read_snpsnap
bg_size	The number of background variant per SNP ID. Default = 200

Details

For each SNP ID, select_background_variants select bg_size number of background variants matched by minor allele frequency, distance to the nearest protein coding gene, and the number of LD proxies (r2>0.7).

Value

A list of data.tables. Each data.table contains the background variant for a SNP ID.

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