Reports 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.

Usage

gl.report.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 NULL, unless specified using gl.set.verbosity].

Value

An unaltered genlight object

Details

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.

Resultant ggplot(s) and the tabulation(s) are saved to the session's temporary directory.

See also

gl.filter.overshoot

Other report functions: gl.report.bases(), gl.report.callrate(), gl.report.diversity(), gl.report.hamming(), gl.report.heterozygosity(), gl.report.hwe(), gl.report.ld.map(), gl.report.locmetric(), gl.report.maf(), gl.report.monomorphs(), gl.report.pa(), gl.report.parent.offspring(), gl.report.rdepth(), gl.report.reproducibility(), gl.report.secondaries(), gl.report.sexlinked(), gl.report.taglength()

Author

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

Examples

gl.report.overshoot(testset.gl)
#> Starting gl.report.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,
#> Completed: gl.report.overshoot 
#> 
#>