gl.report.taglength {dartR.base}

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.display = TRUE,
  plot.theme = theme_dartR(),
  plot.colors = NULL,
  plot.file = NULL,
  plot.dir = NULL,
  verbose = NULL
)

Arguments

x

Name of the genlight object containing the SNP [required].

plot.display

If TRUE, histograms of base composition are displayed in the plot window [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 c("#2171B5", "#6BAED6")].

plot.file

Name for the RDS binary file to save (base name only, exclude extension) [default NULL]

plot.dir

Directory in which to save files [default = working directory]

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. If a plot.file is given, the ggplot arising from this function is saved as an "RDS" binary file using saveRDS(); can be reloaded with readRDS(). A file name must be specified for the plot to be saved. If a plot directory (plot.dir) is specified, the ggplot binary is saved to that directory; otherwise to the tempdir(). 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

Other matched report: gl.report.callrate(), gl.report.hamming(), gl.report.locmetric(), gl.report.maf(), gl.report.overshoot(), gl.report.pa(), gl.report.rdepth(), gl.report.reproducibility(), gl.report.secondaries()

Examples

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