importPolarized {diemr}

Imports genomic data polarized according to the specification

Description

Reads genotypes from a file and changes marker polarity.

Usage

importPolarized(file, changePolarity, ChosenInds)

Arguments

file

character vector with a single path to a file with genotypes.

changePolarity

logical vector with length equal to the number of markers.

ChosenInds

numeric vector of indices of individuals to be included in the analysis.

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.

See Also

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

Examples

dat <- importPolarized(
  file = system.file("extdata", "data6x3.txt", package = "diemr"),
  changePolarity = c(FALSE, TRUE, TRUE),
  ChosenInds = 1:6
)
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" "_"