popPCA: Determines population stratification between different...

In BaderLab/POPPATHR: Population-based pathway analysis of SNP-SNP coevolution

Description

Determines population stratification between different ancestry groups (e.g., CEU vs YRI) via complete linkage clustering

Usage

popPCA(genotype_file, fam_file, pop_one, pop_two, dimensions = 3, output_file)

Arguments

genotype_file	(char) path to PLINK-formatted SNP genotype data.
fam_file	(char) path to population-coded PLINK fam file.
pop_one	(char) character code for the first population (e.g., CEU).
pop_two	(char) character code for the second population (e.g., YRI).
dimensions	(integer) dimensions for which to calculate PCA sim (default=3).
output_file	(char) path to write PNG image.

Value

none

BaderLab/POPPATHR documentation built on Dec. 17, 2021, 9:53 a.m.