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

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 sequence tag length

Description

SNP datasets generated by DArT typically have sequence tag lengths ranging from 20 to 69 base pairs.

Usage

gl.filter.taglength(x, lower = 20, upper = 69, verbose = NULL)

Arguments

x	Name of the genlight object containing the SNP data [required].
lower	Lower threshold value below which loci will be removed [default 20].
upper	Upper threshold value above which loci will be removed [default 69].
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 a sequence tag length in the range specified by the lower and upper threshold.

Author(s)

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

See Also

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.reproducibility(), gl.filter.secondaries(), gl.filter.sexlinked()

Examples

 
# SNP data
  gl.report.taglength(testset.gl)
  result <- gl.filter.taglength(testset.gl,lower=60)
  gl.report.taglength(result)
# Tag P/A data
  gl.report.taglength(testset.gs)
  result <- gl.filter.taglength(testset.gs,lower=60)
  gl.report.taglength(result)
  
  test <- gl.subsample.loci(platypus.gl, n =100)
  res <- gl.report.taglength(test)

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