A utility script to recalculate the frequency of the homozygous reference SNP by locus after some populations have been deleted
The locus metadata supplied by DArT has FreqHomRef included, but the frequency of the homozygous reference will change when some individuals are removed from the dataset.
Name of the genlight object containing the SNP data [required].
Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2].
This script recalculates the FreqHomRef and places these recalculated values in the appropriate place in the genlight object.
Note that the frequency of the homozygote reference SNPS is calculated from the individuals that could be scored.
utils.recalc.metrics for recalculating all metrics,
utils.recalc.callrate for recalculating CallRate,
utils.recalc.avgpic for recalculating AvgPIC,
utils.recalc.freqhomsnp for recalculating frequency of homozygous
utils.recalc.freqhet for recalculating frequency of
gl.recalc.maf for recalculating minor allele frequency,
gl.recalc.rdepth for recalculating average read depth
Custodian: Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)