gl.report.taglength: Reports summary of sequence tag length across loci

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

Reports summary of sequence tag length across loci

Description

SNP datasets generated by DArT typically have sequence tag lengths ranging from 20 to 69 base pairs. This function reports summary statistics of the tag lengths.

Usage

gl.report.taglength(
  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 [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 gl.filter.taglength will filter out the loci with a tag length below a specified threshold.

Quantiles are partitions of a finite set of values into q subsets of (nearly) equal sizes. In this function q = 20. Quantiles are useful measures because they are less susceptible to long-tailed distributions and outliers.

Function's output

The minimum, maximum, mean and a tabulation of tag length quantiles against thresholds are provided. Output also includes a boxplot and a histogram to guide in the selection of a threshold for filtering on tag length.

Plots and table are saved to the temporal directory (tempdir) and can be accessed with the function gl.print.reports and listed with the function gl.list.reports. Note that they can be accessed only in the current R session because tempdir is cleared each time that the R session is closed.

Examples of other themes that can be used can be consulted in

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

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

Value

Returns unaltered genlight object

Author(s)

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

See Also

gl.filter.taglength, gl.list.reports, gl.print.reports

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.parent.offspring(), gl.report.pa(), gl.report.rdepth(), gl.report.reproducibility(), gl.report.secondaries(), gl.report.sexlinked()

Examples

out <- gl.report.taglength(testset.gl)

dartR documentation built on June 8, 2023, 6:48 a.m.