dartR: gl.filter.RepAvg – R documentation

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gl.filter.RepAvg

Filter 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 RepAvg is the proportion of alleles that give a repeatable result, averaged over both alleles for each locus.

Usage

gl.filter.RepAvg(x, threshold = 0.99, 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]
`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

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

Value

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

Author(s)

Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

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)

dartR

Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

v1.9.6

GPL-2

Authors

Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]

Initial release

2021-04-29