check_no_allele {MungeSumstats}R Documentation

Ensure that A1 & A2 are present, if not can find it with SNP and other allele

Description

More care needs to be taken if one of A1/A2 is present, before imputing the other allele flipping needs to be checked

Usage

check_no_allele(sumstats_dt, path, 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)

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]