recodeFAM: Recodes PLINK fam file with population-specific codes

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

Description

Recodes PLINK fam file with population-specific codes

Usage

recodeFAM(
  genotype_file,
  pop_one,
  pop_two,
  population_table,
  SET_SEED = 42,
  output_file = "population-coded"
)

Arguments

genotype_file	(char) path to PLINK-formatted SNP genotype data.
pop_one	(char) character code for the first population (e.g., CEU).
pop_two	(char) character code for the second population (e.g., YRI).
population_table	(char) path to file with population information. Gives the number of samples per population in the dataset.
SET_SEED	(integer) value for set.seed() before shuffling (default=42).
output_file	(char) name for fam file (default=population-coded). File extension added.

Value

none

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