check_frq_maf: Check that FRQ column refers to minor/effect allele frequency...

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Check that FRQ column refers to minor/effect allele frequency not major

Description

Check that FRQ column refers to minor/effect allele frequency not major

Usage

check_frq_maf(sumstats_dt, frq_is_maf)

Arguments

frq_is_maf

Conventionally the FRQ column is intended to show the minor/effect allele frequency (MAF) but sometimes the major allele frequency can be inferred as the FRQ column. This logical variable indicates that the FRQ column should be renamed to MAJOR_ALLELE_FRQ if the frequency values appear to relate to the major allele i.e. >0.5. By default this mapping won't occur i.e. is TRUE.

Value

sumstats_dt, the modified summary statistics data table object

neurogenomics/MungeSumstats documentation built on Aug. 10, 2024, 5:59 a.m.