check_on_ref_genome {MungeSumstats}R Documentation

Ensure all SNPs are on the reference genome

Description

Ensure all SNPs are on the reference genome

Usage

check_on_ref_genome(sumstats_dt, path, ref_genome, on_ref_genome, rsids)

Arguments

sumstats_dt

data table obj of the summary statistics file for the GWAS

path

Filepath for the summary statistics file to be formatted

ref_genome

name of the reference genome used for the GWAS (GRCh37 or GRCh38). Default is GRCh37.

on_ref_genome

Binary Should a check take place that all SNPs are on the reference genome by SNP ID. Default is TRUE

rsids

datatable of snpsById, filtered to SNPs of interest if loaded already. Or else NULL

Value

A list containing two data tables:


[Package MungeSumstats version 1.0.1 Index]