importPolarized: Imports genomic data polarized according to the specification

In diemr: Genome Polarization via Diagnostic Index Expectation Maximization

Imports genomic data polarized according to the specification

Description

Reads genotypes from a file and changes marker polarity.

Usage

importPolarized(
  files,
  changePolarity,
  ChosenInds,
  ChosenSites = "all",
  nCores = 1,
  verbose = FALSE,
  simplify = TRUE,
  ...
)

Arguments

files	A character vector with paths to files with genotypes.
changePolarity	A logical vector or a list of logical vectors with length equal to the number of markers.
ChosenInds	A numeric or logical vector of indices of individuals to be included in the analysis.
ChosenSites	A logical vector indicating which sites are to be included in the analysis.
nCores	A numeric number of cores to be used for parallelisation. Must be nCores = 1 on Windows.
verbose	Logical whether to show messages on import progress.
simplify	Logical. If TRUE, the function returns a matrix.
...	Optional numeric vector of compartmentSizes.

Details

For details on the input data format, check the file with CheckDiemFormat.

The changePolarity argument influences how each marker is imported. Value FALSE means that the marker will be imported as it is saved in the file. Value TRUE means that the genotypes encoded as 0 will be imported as 2, and genotypes encoded in the file as 2 will be imported as 0.

Value

Returns a character matrix with rows containing individual genotypes and columns containing markers. If simplify = FALSE, returns a list of matrices corresponding to compartments in files.

See Also

diem for determining appropriate marker polarity with respect to a barrier to gene flow.

Examples

dat <- importPolarized(
  files <- system.file("extdata", "data7x3.txt", package = "diemr"),
  changePolarity = c(FALSE, TRUE, TRUE),
  ChosenInds = 1:6,
  ChosenSites = "all",
  simplify = TRUE
)
dat
#    m1  m2  m3
# 1 "0" "1" "2"
# 2 "0" "0" "0"
# 3 "1" "1" "0"
# 4 "1" "2" "0"
# 5 "2" "2" "1"
# 6 "2" "2" "_"

diemr documentation built on Dec. 11, 2025, 5:07 p.m.