Filter loci that represent secondary SNPs in a genlight {adegenet} object
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.
gl.filter.secondaries(x, method = "random", verbose = NULL)
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] |
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.
The reduced genlight, plus a summary
Arthur Georges (Post to https://groups.google.com/d/forum/dartr)
gl.report.secondaries(testset.gl) result <- gl.filter.secondaries(testset.gl)
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