utils.recalc.freqhets {dartR.base}

A utility script to recalculate the frequency of the heterozygous SNPs 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.freqhets(x, verbose = NULL)

Arguments

x

Name of the genlight object containing the SNP data [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 FreqHets included, but the frequency of the heterozygotes will change when some individuals are removed from the dataset. This script recalculates the FreqHets 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.freqhomref for recalculating frequency of homozygous reference, utils.recalc.freqhomsnp for recalculating frequency of homozygous alternate, utils.recalc.AvgPIC for recalculating RepAvg, 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.freqhomref(), utils.recalc.freqhomsnp(), utils.recalc.maf(), utils.reset.flags(), utils.transpose()