gl.filter.taglength {dartR.base}

Filters loci in a genlight {adegenet} object based on sequence tag length @family matched filter

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

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)