A utility script to recalculate the frequency of the heterozygous SNPs by locus after some populations have been deleted
Source:R/utils.recalc.freqhets.r
utils.recalc.freqhets.Rd
The locus metadata supplied by DArT has FreqHets included, but the frequency of the heterozygotes will change when some individuals are removed from the dataset.
Details
This script recalculates the FreqHets 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.freqhomref
for recalculating frequency of homozygous
reference, utils.recalc.freqhomsnp
for recalculating frequency of
homozygous alternate,
utils.recalc.AvgPIC
for recalculating RepAvg, 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)