gl.report.reproducibility: Reports summary of RepAvg (repeatability averaged over both...

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Reports summary of RepAvg (repeatability averaged over both alleles for each locus) or reproducibility (repeatability of the scores for fragment presence/absence)

Description

SNP datasets generated by DArT have an index, RepAvg, generated by reproducing the data independently for 30 of alleles that give a repeatable result, averaged over both alleles for each locus.

In the case of fragment presence/absence data (SilicoDArT), repeatability is the percentage of scores that are repeated in the technical replicate dataset.

Usage

gl.report.reproducibility(
  x,
  plot.out = TRUE,
  plot_theme = theme_dartR(),
  plot_colors = two_colors,
  save2tmp = FALSE,
  verbose = NULL
)

Arguments

x	Name of the genlight object containing the SNP or presence/absence (SilicoDArT) data [required].
plot.out	If TRUE, displays a plot to guide the decision on a filter threshold [default TRUE].
plot_theme	Theme for the plot. See Details for options [default theme_dartR()].
plot_colors	List of two color names for the borders and fill of the plots [default two_colors].
save2tmp	If TRUE, saves any ggplots and listings to the session temporary directory (tempdir) [default FALSE].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

Details

The function displays a table of minimum, maximum, mean and quantiles for repeatbility against possible thresholds that might subsequently be specified in gl.filter.reproducibility.

If plot.out=TRUE, display also includes a boxplot and a histogram to guide in the selection of a threshold for filtering on repeatability.

If save2tmp=TRUE, ggplots and relevant tabulations are saved to the session's temp directory (tempdir)

For examples of themes, see:

• https://ggplot2.tidyverse.org/reference/ggtheme.html and

• https://yutannihilation.github.io/allYourFigureAreBelongToUs/ggthemes/

Value

An unaltered genlight object

Author(s)

Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

See Also

gl.filter.reproducibility

Other report functions: gl.report.bases(), gl.report.callrate(), gl.report.diversity(), gl.report.hamming(), gl.report.heterozygosity(), gl.report.hwe(), gl.report.ld.map(), gl.report.locmetric(), gl.report.maf(), gl.report.monomorphs(), gl.report.overshoot(), gl.report.pa(), gl.report.parent.offspring(), gl.report.rdepth(), gl.report.secondaries(), gl.report.sexlinked(), gl.report.taglength()

Examples

 
# SNP data
  out <- gl.report.reproducibility(testset.gl)
  
# Tag P/A data
  out <- gl.report.reproducibility(testset.gs)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.