gl.filter.reproducibility: Filters loci in a genlight {adegenet} object based on average...

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

Filters loci in a genlight {adegenet} object based on average repeatability of alleles at a locus

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.out = TRUE,
  plot_theme = theme_dartR(),
  plot_colors = two_colors,
  save2tmp = FALSE,
  verbose = NULL
)

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.out	If TRUE, displays a plots of the distribution of reproducibility values before and after filtering [default TRUE].
plot_theme	Theme for the plot [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].

Value

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

Author(s)

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

See Also

gl.report.reproducibility

Other filter functions: gl.filter.allna(), gl.filter.callrate(), gl.filter.heterozygosity(), gl.filter.hwe(), gl.filter.ld(), gl.filter.locmetric(), gl.filter.maf(), gl.filter.monomorphs(), gl.filter.overshoot(), gl.filter.parent.offspring(), gl.filter.pa(), gl.filter.rdepth(), gl.filter.secondaries(), gl.filter.sexlinked(), gl.filter.taglength()

Examples

 
# 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)
  
  
  test <- gl.subsample.loci(platypus.gl,n=100)
  res <- gl.filter.reproducibility(test)
  

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