A utility script to recalculate the frequency of the homozygous reference SNP by locus after some populations have been deleted
Source:R/utils.recalc.freqhomref.r
utils.recalc.freqhomref.Rd
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.
Details
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.
See also
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
alternate, utils.recalc.freqhet
for recalculating frequency of
heterozygotes, gl.recalc.maf
for recalculating minor allele frequency,
gl.recalc.rdepth
for recalculating average read depth
Author
Custodian: Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)