utils.recalc.freqhomref {dartR} | R Documentation |
A utility script to recalculate the frequency of the homozygous reference SNP by locus after some populations have been deleted
Description
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.
Usage
utils.recalc.freqhomref(x, verbose = NULL)
Arguments
x |
Name of the genlight object containing the SNP data [required]. |
verbose |
Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2]. |
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.
Value
The modified genlight object
Author(s)
Custodian: Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)
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
Examples
#result <- utils.recalc.freqhomref(testset.gl)