dartR: gl.report.overshoot – R documentation

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gl.report.overshoot

Reports 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.

Usage

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

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 or as specified using gl.set.verbosity]

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.

Value

returns names of the recalcitrant loci

Author(s)

Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

Examples

out <- gl.report.overshoot(testset.gl)

dartR

Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

v1.9.6

GPL-2

Authors

Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]

Initial release

2021-04-29