utils.reset.flags {dartR.base}

#' An internal utility function to reset to FALSE (or TRUE) the locus metric flags after some individuals or populations have been deleted.

Description

WARNING: UTILITY SCRIPTS ARE FOR INTERNAL USE ONLY AND SHOULD NOT BE USED BY END USERS AS THEIR USE OUT OF CONTEXT COULD LEAD TO UNPREDICTABLE OUTCOMES.

Usage

utils.reset.flags(x, set = FALSE, value = 2, verbose = NULL)

Arguments

x

Name of the genlight object [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 2 or as specified using gl.set.verbosity]

Details

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 This script resets the locus metrics flags to FALSE to indicate that these statistics in the genlight object are no longer current.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. 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).

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

Other utilities: gl.alf(), utils.check.datatype(), utils.dart2genlight(), utils.dist.binary(), utils.flag.start(), utils.hamming(), utils.het.pop(), utils.impute, utils.is.fixed(), utils.jackknife(), utils.n.var.invariant(), utils.plot.save(), utils.read.fasta(), utils.read.ped(), utils.recalc.avgpic(), utils.recalc.callrate(), utils.recalc.freqhets(), utils.recalc.freqhomref(), utils.recalc.freqhomsnp(), utils.recalc.maf(), utils.transpose()

Examples

result <- utils.reset.flags(testset.gl)