Read genotype data from EIGENSTRAT files — read

Read genotype data from EIGENSTRAT files

read_eigenstrat(
  pref,
  inds = NULL,
  pops = NULL,
  first = 1,
  last = Inf,
  transpose = FALSE,
  verbose = TRUE
)

Arguments

pref: Prefix of the packedancestrymap files
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'
first: Index of first SNP to read
last: Index of last SNP to read
transpose: Transpose genotype matrix (default is snps x individuals)
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)
}