Reports monomorphic loci

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].

Value

An unaltered genlight object

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)

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.pa(), gl.report.parent.offspring(), gl.report.rdepth(), gl.report.reproducibility(), gl.report.secondaries(), gl.report.sexlinked(), gl.report.taglength()

Author

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

Examples

# SNP data
  gl.report.monomorphs(testset.gl)
#> Starting gl.report.monomorphs 
#>   Processing genlight object with SNP data
#>   Identifying monomorphic loci
#> 
#>   No. of loci: 255 
#>     Polymorphic loci: 111 
#>     Monomorphic loci: 144 
#>     Loci scored all NA: 0 
#>   No. of individuals: 250 
#>   No. of populations: 30 
#> 
#> Completed: gl.report.monomorphs 
#> 
# SilicoDArT data
  gl.report.monomorphs(testset.gs)
#> Starting gl.report.monomorphs 
#>   Processing genlight object with Presence/Absence (SilicoDArT) data
#>   Identifying monomorphic loci
#> 
#>   No. of loci: 255 
#>     Polymorphic loci: 214 
#>     Monomorphic loci: 41 
#>     Loci scored all NA: 0 
#>   No. of individuals: 218 
#>   No. of populations: 29 
#> 
#> Completed: gl.report.monomorphs 
#>