dartR (version 1.9.9.1)

gl.report.monomorphs: Report monomorphic loci

Description

This script reports the number of monomorphic locim and those with all NAsm from 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 2 or as 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)

Examples

# NOT RUN {
# SNP data
  out <- gl.report.monomorphs(testset.gl)
# SilicoDArT data
  out <- gl.report.monomorphs(testset.gs)
# }