#' A utility script to recalculate the minor allele frequency by locus,
#' typically after some populations have been deleted
#'
#' The locus metadata supplied by DArT does not have MAF included, so it is
#' calculated and added to the locus.metadata by this script. The minimum allele
#' frequency will change when some individuals are removed from the dataset.
#' This script recalculates the MAF and places these recalculated values in the
#' appropriate place in the genlight object.
#'
#' @param x Name of the genlight object containing the SNP data [required].
#' @param verbose Verbosity: 0, silent or fatal errors; 1, begin and end; 2,
#' progress log; 3, progress and results summary; 5, full report [default 2].
#' @return The modified genlight dataset.
#' @author Custodian: Luis Mijangos (Post to
#' \url{https://groups.google.com/d/forum/dartr})
#' @seealso \code{utils.recalc.metrics} for recalculating all metrics,
#' \code{utils.recalc.callrate} for recalculating CallRate,
#' \code{utils.recalc.freqhomref} for recalculating frequency of homozygous
#' reference, \code{utils.recalc.freqhomsnp} for recalculating frequency of
#' homozygous alternate, \code{utils.recalc.freqhet} for recalculating frequency
#' of heterozygotes, \code{gl.recalc.avgpic} for recalculating AvgPIC,
#' \code{gl.recalc.rdepth} for recalculating average read depth
#' @examples
#' #f <- dartR::utils.recalc.maf(testset.gl)
utils.recalc.maf <- function(x,
verbose = NULL) {
# SET VERBOSITY
verbose <- gl.check.verbosity(verbose)
# FLAG SCRIPT START
funname <- match.call()[[1]]
utils.flag.start(func = funname,
build = "Jody",
verbosity = verbose)
# CHECK DATATYPE
datatype <- utils.check.datatype(x, verbose = verbose)
# Check monomorphs have been removed up to date
if (x@other$loc.metrics.flags$monomorphs == FALSE) {
if (verbose >= 2) {
cat(
warn(
" Warning: Dataset contains monomorphic loci which will be included in the ",
funname,
" calculations\n"
)
)
}
}
# FUNCTION SPECIFIC ERROR CHECKING
if (is.null(x@other$loc.metrics$maf)) {
if (verbose >= 3) {
cat(
report(
" Locus metric maf does not exist, creating slot @other$loc.metrics$maf\n"
)
)
}
x@other$loc.metrics$maf <- array(NA, nLoc(x))
}
# DO THE JOB
if (verbose >= 2) {
cat(report(" Recalculating FreqHoms and FreqHets\n"))
}
x <- utils.recalc.freqhets(x, verbose = verbose)
x <- utils.recalc.freqhomref(x, verbose = verbose)
x <- utils.recalc.freqhomsnp(x, verbose = verbose)
# Calculate and plot overall MAF
if (verbose >= 2) {
cat(report(" Recalculating Minor Allele Frequency (MAF)\n"))
}
alf <- gl.alf(x)[, 2]
x@other$loc.metrics$maf <- ifelse(alf > 0.5, 1 - alf, alf)
x@other$loc.metrics.flags$maf <- TRUE
# FLAG SCRIPT END
if (verbose > 0) {
cat(report("Completed:", funname, "\n"))
}
return(x)
}
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