gl.filter.pa: Filters loci that contain private (and fixed alleles) between...

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

Filters loci that contain private (and fixed alleles) between two populations

Description

This script is meant to be used prior to gl.nhybrids to maximise the information content of the SNPs used to identify hybrids (currently newhybrids does allow only 200 SNPs). The idea is to use first all loci that have fixed alleles between the potential source populations and then 'fill up' to 200 loci using loci that have private alleles between those. The functions filters for those loci (if invers is set to TRUE, the opposite is returned (all loci that are not fixed and have no private alleles - not sure why yet, but maybe useful.)

Usage

gl.filter.pa(x, pop1, pop2, invers = FALSE, verbose = NULL)

Arguments

x	Name of the genlight object containing the SNP data [required].
pop1	Name of the first parental population (in quotes) [required].
pop2	Name of the second parental population (in quotes) [required].
invers	Switch to filter for all loci that have no private alleles and are not fixed [FALSE].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

Value

The reduced genlight dataset, containing now only fixed and private alleles.

Author(s)

Authors: Bernd Gruber & Ella Kelly (University of Melbourne); Custodian: Luis Mijangos – Post to https://groups.google.com/d/forum/dartr

See Also

Other filter functions: gl.filter.allna(), gl.filter.callrate(), gl.filter.heterozygosity(), gl.filter.hwe(), gl.filter.ld(), gl.filter.locmetric(), gl.filter.maf(), gl.filter.monomorphs(), gl.filter.overshoot(), gl.filter.parent.offspring(), gl.filter.rdepth(), gl.filter.reproducibility(), gl.filter.secondaries(), gl.filter.sexlinked(), gl.filter.taglength()

Examples

result <- gl.filter.pa(testset.gl, pop1=pop(testset.gl)[1], 
pop2=pop(testset.gl)[2],verbose=3)

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