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This script reports the number of monomorphic loci and those with all NAs in a genlight {adegenet} object
gl.report.monomorphs(x, verbose = NULL)An unaltered genlight object
Name of the input genlight object [required].
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].
Custodian: Arthur Georges -- Post to https://groups.google.com/d/forum/dartr
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)
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()
# SNP data
gl.report.monomorphs(testset.gl)
# SilicoDArT data
gl.report.monomorphs(testset.gs)
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