gl.filter.monomorphs: Filters monomorphic loci, including those with all NAs

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

Filters monomorphic loci, including those with all NAs

Description

This script deletes monomorphic loci from a genlight {adegenet} object

A DArT dataset will not have monomorphic loci, but they can arise, along with loci that are scored all NA, when populations or individuals are deleted.

Retaining monomorphic loci unnecessarily increases the size of the dataset and will affect some calculations.

Note that for SNP data, NAs likely represent null alleles; in tag presence/absence data, NAs represent missing values (presence/absence could not be reliably scored)

Usage

gl.filter.monomorphs(x, verbose = NULL)

Arguments

x	Name of the input 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, unless specified using gl.set.verbosity].

Value

A genlight object with monomorphic (and all NA) loci removed.

Author(s)

Custodian: Arthur Georges – 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.overshoot(), gl.filter.parent.offspring(), gl.filter.pa(), gl.filter.rdepth(), gl.filter.reproducibility(), gl.filter.secondaries(), gl.filter.sexlinked(), gl.filter.taglength()

Examples

# SNP data
  result <- gl.filter.monomorphs(testset.gl, verbose=3)
# Tag P/A data
  result <- gl.filter.monomorphs(testset.gs, verbose=3)

dartR documentation built on June 8, 2023, 6:48 a.m.