utils.recalc.avgpic {dartR} | R Documentation |
A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC by locus after some individuals or populations have been deleted.
Description
The locus metadata supplied by DArT has OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC included, but the allelic composition will change when some individuals,or populations, are removed from the dataset and so the initial statistics will no longer apply. This script recalculates these statistics and places the recalculated values in the appropriate place in the genlight object.
Usage
utils.recalc.avgpic(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
If the locus metadata OneRatioRef|Snp, PICRef|Snp and/or AvgPIC do not exist, the script creates and populates them.
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.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.maf
for recalculating minor allele
frequency, gl.recalc.rdepth
for recalculating average read depth
Examples
#out <- utils.recalc.avgpic(testset.gl)