utils.recalc.avgpic: A utility script to recalculate the OneRatioRef, OneRatioSnp,...

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC by locus after some individuals or populations have been deleted.

Description

The locus metadata supplied by DArT has OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC included, but the allelic composition will change when some individuals,or populations, are removed from the dataset and so the initial statistics will no longer apply. This script recalculates these statistics and places the recalculated values in the appropriate place in the genlight object.

Usage

utils.recalc.avgpic(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].

Details

If the locus metadata OneRatioRef|Snp, PICRef|Snp and/or AvgPIC do not exist, the script creates and populates them.

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.freqhet for recalculating frequency of heterozygotes, gl.recalc.maf for recalculating minor allele frequency, gl.recalc.rdepth for recalculating average read depth

Examples

#out <- utils.recalc.avgpic(testset.gl)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.