extract_samples: Extract samples from PLINK files
In uqrmaie1/admixtools: Inferring demographic history from genetic data

extract_samples

R Documentation

Extract samples from PLINK files

Description

This function reads PLINK files, extracts a subset of samples, and writes new PLINK files using write_plink. It's probably slower than running the equivalent command in PLINK directly, but it can be useful to do this from within R. When inds or pops is provided, only a subset of samples will be extracted.

Usage

extract_samples(
  inpref,
  outpref,
  inds = NULL,
  pops = NULL,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

`inpref`	Prefix of the PLINK input files
`outpref`	Prefix of the PLINK output files
`inds`	Individuals which should be extracted
`pops`	Populations which should be extracted. Can not be provided together with `inds`
`overwrite`	Set this to `TRUE` if `inpref == outpref` and you really want to overwrite the input files.
`verbose`	Print progress updates