| gl.filter.secondaries {dartR.base} | R Documentation |
Filters loci that represent secondary SNPs in a genlight 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. 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.
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' [default '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 genlight object, with the secondary SNP loci removed.
Author(s)
Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr
See Also
Other matched filter:
gl.filter.callrate(),
gl.filter.hamming(),
gl.filter.ld(),
gl.filter.locmetric(),
gl.filter.maf(),
gl.filter.monomorphs(),
gl.filter.overshoot(),
gl.filter.pa()
Examples
gl.report.secondaries(testset.gl)
result <- gl.filter.secondaries(testset.gl)