utils.recalc.freqhomref {dartR.base}

#' An internal utility function to recalculate the frequency of the homozygous reference SNP by locus after some populations have been deleted

Description

WARNING: UTILITY SCRIPTS ARE FOR INTERNAL USE ONLY AND SHOULD NOT BE USED BY END USERS AS THEIR USE OUT OF CONTEXT COULD LEAD TO UNPREDICTABLE OUTCOMES.

Usage

utils.recalc.freqhomref(x, verbose = NULL)

Arguments

x

Name of the genlight [required].

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]

Details

The locus metadata supplied by DArT has FreqHomRef included, but the frequency of the homozygous reference will change when some individuals are removed from the dataset. This script recalculates the FreqHomRef and places these recalculated values in the appropriate place in the genlight object. Note that the frequency of the homozygote reference SNPS is calculated from the individuals that could be scored.

Value

The modified genlight object

Author(s)

Custodian: Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)

See Also

utils.recalc.metrics for recalculating all metrics, utils.recalc.callrate for recalculating CallRate, utils.recalc.avgpic for recalculating AvgPIC, utils.recalc.freqhomsnp for recalculating frequency of homozygous alternate, utils.recalc.freqhet for recalculating frequency of heterozygotes, gl.recalc.maf for recalculating minor allele frequency, gl.recalc.rdepth for recalculating average read depth

Other utilities: gl.alf(), utils.check.datatype(), utils.dart2genlight(), utils.dist.binary(), utils.flag.start(), utils.hamming(), utils.het.pop(), utils.impute, utils.is.fixed(), utils.jackknife(), utils.n.var.invariant(), utils.plot.save(), utils.read.fasta(), utils.read.ped(), utils.recalc.avgpic(), utils.recalc.callrate(), utils.recalc.freqhets(), utils.recalc.freqhomsnp(), utils.recalc.maf(), utils.reset.flags(), utils.transpose()