Read genotype data from PLINK files — read

See genio for a dedicated R package for reading and writing PLINK files. This function is based on a similar function in the plink2R package.

read_plink(pref, inds = NULL, pops = NULL, verbose = FALSE)

Arguments

pref: Prefix of packedancestrymap files (files have to end in .geno, .ind, .snp)
inds: Individuals for which data should be read. Defaults to all individuals
pops: Populations for which data should be read. Cannot be provided together with 'inds'
verbose: Print progress updates

A list with the genotype data matrix, the .ind file, and the .snp file

if (FALSE) {
samples = c('Ind1', 'Ind2', 'Ind3')
geno = read_packedancestrymap(prefix, samples)
}