R/gl.report.overshoot.r
gl.report.overshoot.RdThis 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.
gl.report.overshoot(x, save2tmp = FALSE, verbose = NULL)Name of the genlight object [required].
If TRUE, saves any ggplots and listings to the session temporary directory (tempdir) [default FALSE].
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].
An unaltered genlight object
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.
Other report functions:
gl.report.bases(),
gl.report.callrate(),
gl.report.diversity(),
gl.report.hamming(),
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.replicates(),
gl.report.reproducibility(),
gl.report.secondaries(),
gl.report.sexlinked(),
gl.report.taglength()
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
#>
#>