utils.recalc.freqhomsnp: A utility function to recalculate the frequency of the...

In dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions

A utility function to recalculate the frequency of the homozygous alternate 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.freqhomsnp(x, verbose = NULL)

Arguments

x	Name of the genlight object [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 FreqHomSnp included, but the frequency of the homozygous alternate will change when some individuals are removed from the dataset. This function recalculates the FreqHomSnp and places these recalculated values in the appropriate place in the genlight object. Note that the frequency of the homozygote alternate SNPS is calculated from the individuals that could be scored. This function only applies to SNP genotype data not Tag P/A data (SilicoDArT).

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.avgpic for recalculating AvgPIC, 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.collapse.matrix(), 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.freqhomref(), utils.recalc.maf(), utils.reset.flags(), utils.transpose(), utils.vcfr2genlight.polyploid()

dartR.base documentation built on April 4, 2025, 2:45 a.m.