dartR (version 1.9.9.1)

gl.filter.secondaries: Filter loci that represent secondary SNPs in a genlight {adegenet} object

Description

SNP datasets generated by DArT include fragments with more than one SNP and record them separately with the same CloneID (=AlleleID). These multiple SNP loci within a fragment (secondaries) are likely to be linked, and so you may wish to remove secondaries.

Usage

gl.filter.secondaries(x, method = "random", verbose = NULL)

Arguments

x

-- name of the genlight object containing the SNP data [required]

method

-- method of selecting SNP locus to retain, best or random [random]

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

The reduced genlight, plus a summary

Details

This script filters out all but the first sequence tag with the same CloneID after ordering the genlight object on based on repeatability, avgPIC in that order (method="best") or at random (method="random").

The filter has not been implemented for tag presence/absence data.

Examples

# NOT RUN {
gl.report.secondaries(testset.gl)
result <- gl.filter.secondaries(testset.gl)
# }