gl.report.callrate {dartR}

Reports summary of Call Rate for loci or individuals

Description

SNP datasets generated by DArT have missing values primarily arising from failure to call a SNP because of a mutation at one or both of the restriction enzyme recognition sites. P/A datasets (SilicoDArT) have missing values because it was not possible to call whether a sequence tag was amplified or not. This function tabulates the number of missing values as quantiles.

Usage

gl.report.callrate(
  x,
  method = "loc",
  by_pop = FALSE,
  plot.out = TRUE,
  plot_theme = theme_dartR(),
  plot_colors = two_colors,
  bins = 50,
  save2tmp = FALSE,
  verbose = NULL
)

Arguments

x

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

method

Specify the type of report by locus (method='loc') or individual (method='ind') [default 'loc'].

by_pop

Whether report by population [default FALSE].

plot.out

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 two_colors].

bins

Number of bins to display in histograms [default 25].

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

This function expects a genlight object, containing either SNP data or SilicoDArT (=presence/absence data).

Callrate is summarized by locus or by individual to allow sensible decisions on thresholds for filtering taking into consideration consequential loss of data. The summary is in the form of a tabulation and plots.

Plot themes can be obtained from:

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

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

Resultant ggplots and the tabulation are saved to the session's temporary directory.

Value

Returns unaltered genlight object

Author(s)

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

See Also

gl.filter.callrate

Other report functions: gl.report.bases(), 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(), gl.report.taglength()

Examples

 
# SNP data
  test.gl <- testset.gl[1:20,]
  gl.report.callrate(test.gl)
  gl.report.callrate(test.gl,method='ind')
# Tag P/A data
  test.gs <- testset.gs[1:20,]
  gl.report.callrate(test.gs)
  gl.report.callrate(test.gs,method='ind')
  
  test.gl <- testset.gl[1:20,]
  gl.report.callrate(test.gl)