Filters loci for which the SNP has been trimmed from the sequence tag along with the adaptor

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, save2tmp = FALSE, verbose = NULL)

Arguments

x

Name of the genlight object [required].

save2tmp

If TRUE, saves any ggplots and listings to the session temporary directory (tempdir) [default FALSE].

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

A new genlight object with the recalcitrant loci deleted

See also

Other filter functions: gl.filter.allna(), gl.filter.callrate(), gl.filter.heterozygosity(), gl.filter.hwe(), gl.filter.ld(), gl.filter.locmetric(), gl.filter.maf(), gl.filter.monomorphs(), gl.filter.parent.offspring(), gl.filter.pa(), gl.filter.rdepth(), gl.filter.reproducibility(), gl.filter.secondaries(), gl.filter.sexlinked(), gl.filter.taglength()

Author

Custodian: Arthur Georges -- Post to https://groups.google.com/d/forum/dartr

Examples

result <- gl.filter.overshoot(testset.gl, verbose=3)
#> Starting gl.filter.overshoot 
#>   Processing genlight object with SNP data
#>   Identifying loci for which the SNP has been trimmed with the 
#>             adaptor
#>   No. of loci with SNP falling outside the trimmed sequence: 21 
#> 100050384-49-C/G, 100051015-65-C/T, 100051776-48-T/C, 100052415-21-A/G, 100053200-49-A/T, 100055842-39-G/A, 100056649-23-A/C, 100057527-48-A/G, 100060562-41-T/G, 100061517-51-T/C, 100067093-24-A/G, 100097015-9-G/T, 100097031-40-T/C, 100097429-15-T/C, 100097451-8-G/T, 100097541-14-G/A, 100097604-7-C/G, 100097607-15-C/T, 100097869-7-G/C, 100112469-19-C/T, 100114332-43-A/G,
#>   Deleting those loci
#> Completed: gl.filter.overshoot 
#>