gl.report.rdepth {dartR.base}

Reports summary of Read Depth for each locus

Description

SNP datasets generated by DArT report AvgCountRef and AvgCountSnp as counts of sequence tags for the reference and alternate alleles respectively. These can be used to back calculate Read Depth. Fragment presence/absence datasets as provided by DArT (SilicoDArT) provide Average Read Depth and Standard Deviation of Read Depth as standard columns in their report. This function reports the read depth by locus for each of several quantiles.

Usage

gl.report.rdepth(
  x,
  plot.display = TRUE,
  plot.theme = theme_dartR(),
  plot.colors = NULL,
  plot.dir = NULL,
  plot.file = NULL,
  verbose = NULL
)

Arguments

x

Name of the genlight object containing the SNP or presence/absence (SilicoDArT) data [required].

plot.display

Specify if plot is to be produced [default TRUE].

plot.theme

User specified theme [default theme_dartR()].

plot.colors

Vector with two color names for the borders and fill [default c("#2171B5", "#6BAED6")].

plot.dir

Directory to save the plot RDS files [default as specified by the global working directory or tempdir()]

plot.file

Filename (minus extension) for the RDS plot file [Required for plot save]

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 read depth against possible thresholds that might subsequently be specified in gl.filter.rdepth. If plot.display=TRUE, display also includes a boxplot and a histogram to guide in the selection of a threshold for filtering on read depth. Plot colours can be set with gl.select.colors(). If plot.file is specified, plots are saved to the directory specified by the user, or the global default working directory set by gl.set.wd() or to the 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.rdepth

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

Examples

# SNP data
df <- gl.report.rdepth(testset.gl)
df <- gl.report.rdepth(testset.gs)