genepop_filter_maf: Filters genepop file for MAF

In rystanley/genepopedit: Simple and flexible manipulation of genomic data

Filters genepop file for MAF

Description

Converts genepop file to PED and filters for MAF using plink and returns genepop file with only SNPs that pass filter

Usage

genepop_filter_maf(genepop, where.plink, where.pgdspider, maf = 0.05,
  path)

Arguments

genepop	A file path to the genepop format file you wish to filter.
where.plink	A file path to the PLINK installation folder.
where.pgdspider	A file path to the PGDspider installation folder.
maf	Minor allele frequency cutoff (default = 0.05).
path	file path to directory where the output will be saved.

rystanley/genepopedit documentation built on June 27, 2023, 11:33 p.m.