A utility script to recalculate the minor allele frequency by locus, typically after some populations have been deleted
Source:R/utils.recalc.maf.r
utils.recalc.maf.Rd
The locus metadata supplied by DArT does not have MAF included, so it is calculated and added to the locus.metadata by this script. The minimum allele frequency will change when some individuals are removed from the dataset. This script recalculates the MAF and places these recalculated values in the appropriate place in the genlight object.
See also
utils.recalc.metrics
for recalculating all metrics,
utils.recalc.callrate
for recalculating CallRate,
utils.recalc.freqhomref
for recalculating frequency of homozygous
reference, utils.recalc.freqhomsnp
for recalculating frequency of
homozygous alternate, utils.recalc.freqhet
for recalculating frequency
of heterozygotes, gl.recalc.avgpic
for recalculating AvgPIC,
gl.recalc.rdepth
for recalculating average read depth
Author
Custodian: Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)