dartR.base (version 1.0.5)

gl.filter.overshoot: Filters loci for which the SNP has been trimmed from the sequence tag along with the adaptor

Description

This function checks the position of the SNP within the trimmed sequence tag and identifies those for which the SNP position is outside the trimmed sequence tag. This can happen, rarely, when the sequence containing the SNP resembles the adaptor. The SNP genotype can still be used in most analyses, but functions like gl2fasta() will present challenges if the SNP has been trimmed from the sequence tag. Not fatal, but should apply this filter before gl.filter.secondaries, for obvious reasons.

Usage

gl.filter.overshoot(x, verbose = NULL)

Value

A new genlight object with the recalcitrant loci deleted

Arguments

x

Name of the genlight object [required].

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].

Author

Author(s): Arthur Georges; 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.pa(), gl.filter.secondaries()

Examples

result <- gl.filter.overshoot(testset.gl, verbose=3)