dartR (version 1.9.9.1)

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]

Value

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

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.

Examples

# NOT RUN {
# 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)
# }