A utility script to recalculate the callrate by locus after some populations have been deleted
SNP datasets generated by DArT have missing values primarily arising from failure to call a SNP because of a mutation at one or both of the restriction enzyme recognition sites. The locus metadata supplied by DArT has callrate included, but the call rate will change when some individuals are removed from the dataset. This script recalculates the callrate and places these recalculated values in the appropriate place in the genlight object. It sets the Call Rate flag to TRUE.
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].
utils.recalc.metrics for recalculating all metrics,
utils.recalc.avgpic for recalculating avgPIC,
utils.recalc.freqhomref for recalculating frequency of homozygous
utils.recalc.freqhomsnp for recalculating frequency of
utils.recalc.freqhet for recalculating frequency
gl.recalc.maf for recalculating minor allele
gl.recalc.rdepth for recalculating average read depth
Custodian: Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)