utils.recalc.maf {dartR} | R Documentation |
A utility script to recalculate the minor allele frequency by locus, typically after some populations have been deleted
Description
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.
Usage
utils.recalc.maf(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]. |
Value
The modified genlight dataset.
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.avgpic
for recalculating AvgPIC,
gl.recalc.rdepth
for recalculating average read depth
Examples
#f <- dartR::utils.recalc.maf(testset.gl)