importPolarized {diemr} | R Documentation |
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,
...
)
Arguments
files |
character vector with paths to files 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. |
ChosenSites |
logical vector indicating which sites are to be included in the analysis. |
nCores |
numeric. Number of cores to be used for parallelisation. Must be
at most equal to the number of files in the |
verbose |
logical whether to show messages on import progress. |
... |
optional numeric vector of |
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(
files = system.file("extdata", "data7x3.txt", package = "diemr"),
changePolarity = c(FALSE, TRUE, TRUE),
ChosenInds = 1:6,
ChosenSites = "all"
)
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" "_"