read_regenie: Read REGENIE results files into R

In rmgpanw/rlgenetics: Utility functions for genetic analyses

Description

Reads .regenie GWAS results files into a data table in R, filtering on minor allele frequency (appended) and info score. Also appends a p value column (P).

Usage

read_regenie(path, maf_threshold = 0.01, info_threshold = 0.9)

Arguments

path	File path to directory containing .regenie files. There should be one file for each of 22 chromosomes (i.e. excluding sex chromosomes), otherwise and error is raised. An error is also raised if the column names do not match those expected for REGENIE: 'CHROM', 'GENPOS', 'ID', 'ALLELE0', 'ALLELE1', 'A1FREQ', 'INFO', 'N', 'TEST', 'BETA', 'SE', 'CHISQ', 'LOG10P', 'EXTRA'.
maf_threshold	Minor allele frequencies below this threshold will be removed. Default is 0.01.
info_threshold	Info scores below this threshold will be removed. Default is 0.9.

Value

A data table.

rmgpanw/rlgenetics documentation built on Jan. 6, 2022, 12:32 a.m.