Filters loci that contain private (and fixed alleles) between two populations
Source:R/gl.filter.pa.r
gl.filter.pa.Rd
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.)
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].
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()
Author
Authors: Bernd Gruber & Ella Kelly (University of Melbourne); Custodian: Luis Mijangos – Post to https://groups.google.com/d/forum/dartr