A utility script to reset to FALSE (or TRUE) the locus metric flags after some individuals or populations have been deleted.
Source:R/utils.reset.flags.r
utils.reset.flags.Rd
The locus metadata supplied by DArT has OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC included, but the allelic composition will change when some individuals are removed from the dataset and so the initial statistics will no longer apply. This applies also to some variable calculated by dartR (e.g. maf). This script resets the locus metrics flags to FALSE to indicate that these statistics in the genlight object are no longer current. The verbosity default is also set, and in the case of SilcoDArT, the flags PIC and OneRatio are also set.
Arguments
- x
Name of the genlight object containing the SNP data or tag presence/absence data (SilicoDArT) [required].
- set
Set the flags to TRUE or FALSE [default FALSE].
- value
Set the default verbosity for all functions, where verbosity is not specified [default 2].
- verbose
Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default NULL].
Details
If the locus metrics do not exist then they are added to the genlight object but not populated. If the locus metrics flags do not exist, then they are added to the genlight object and set to FALSE (or TRUE).
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
Author
Custodian: Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)