utils.reset.flags: A utility script to reset to FALSE (or TRUE) the locus metric...
In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis
View source: R/utils.reset.flags.r
utils.reset.flags R Documentation
A utility script to reset to FALSE (or TRUE) the locus metric flags 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 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that these statistics in the genlight object are no longer current.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.
Usage
utils.reset.flags(x, set = FALSE, value = 2, verbose = NULL)
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).
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
#result <- utils.reset.flags(testset.gl)
dartR documentation built on June 8, 2023, 6:48 a.m.
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View source: R/utils.reset.flags.r
| utils.reset.flags | R Documentation |
A utility script to reset to FALSE (or TRUE) the locus metric flags 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 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.
Usage
utils.reset.flags(x, set = FALSE, value = 2, verbose = NULL)
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).
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
#result <- utils.reset.flags(testset.gl)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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