gl.filter.reproducibility: Filters loci in a genlight {adegenet} object based on average repeatability of alleles at a locus @family matched filter

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. SilicoDArT datasets generated by DArT have a similar index, Reproducibility. For these fragment presence/absence data, repeatability is the percentage of scores that are repeated in the technical replicate dataset.

Usage

gl.filter.reproducibility(
  x,
  threshold = 0.99,
  plot.display = TRUE,
  plot.theme = theme_dartR(),
  plot.colors = NULL,
  plot.file = NULL,
  plot.dir = NULL,
  verbose = NULL
)

Value

Returns a genlight object retaining loci with repeatability (Repavg or Reproducibility) greater than the specified threshold.

Arguments

x: Name of the genlight object containing the SNP data [required].
threshold: Threshold value below which loci will be removed [default 0.99].
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].

Author

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

Examples

Run this code

 # \donttest{
# SNP data
  gl.report.reproducibility(testset.gl)
  result <- gl.filter.reproducibility(testset.gl, threshold=0.99, verbose=3)
# Tag P/A data
  gl.report.reproducibility(testset.gs)
  result <- gl.filter.reproducibility(testset.gs, threshold=0.99)
  # }
  res <- gl.filter.reproducibility(testset.gl)