gl.report.monomorphs: Reports monomorphic loci

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

Reports monomorphic loci

Description

This script reports the number of monomorphic loci and those with all NAs in a genlight {adegenet} object

Usage

gl.report.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 NULL, unless specified using gl.set.verbosity].

Details

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)

Value

An unaltered genlight object

Author(s)

Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

See Also

gl.filter.monomorphs

Other report functions: gl.report.bases(), gl.report.callrate(), gl.report.diversity(), gl.report.hamming(), gl.report.heterozygosity(), gl.report.hwe(), gl.report.ld.map(), gl.report.locmetric(), gl.report.maf(), gl.report.overshoot(), gl.report.parent.offspring(), gl.report.pa(), gl.report.rdepth(), gl.report.reproducibility(), gl.report.secondaries(), gl.report.sexlinked(), gl.report.taglength()

Examples

# SNP data
  gl.report.monomorphs(testset.gl)
# SilicoDArT data
  gl.report.monomorphs(testset.gs)

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