utils.recalc.maf: A utility script to recalculate the minor allele frequency by...

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 minor allele frequency by locus, typically after some populations have been deleted

Description

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.

Usage

utils.recalc.maf(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].

Value

The modified genlight dataset.

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.avgpic for recalculating AvgPIC, gl.recalc.rdepth for recalculating average read depth

Examples

#f <- dartR::utils.recalc.maf(testset.gl)

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