| gl.report.overshoot {dartR.base} | R Documentation |
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 NULL, unless 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. Resultant ggplot(s) and the tabulation(s) are saved to the session's temporary directory.
Value
An unaltered genlight object
Author(s)
Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr
See Also
Other matched report:
gl.report.callrate(),
gl.report.hamming(),
gl.report.locmetric(),
gl.report.maf(),
gl.report.pa(),
gl.report.rdepth(),
gl.report.reproducibility(),
gl.report.secondaries(),
gl.report.taglength()
Examples
gl.report.overshoot(testset.gl)