dartR: gl.compliance.check – R documentation

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gl.compliance.check

Checks a gl object to see if it complies with dartR expectations, and amends to comply if necessary

Description

A genlight object used by dartR has a number of requirements that allow functions within the package to operate correctly. The genlight object comprises

Usage

gl.compliance.check(x, verbose = NULL)

Arguments

`x`	– name of the input 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

(a) The SNP genotypes or Tag Presence/Absence data (SilicoDArT); (b) An associated dataframe (gl@other$loc.metrics) containing the locus metrics (e.g. Call Rate, Repeatability, etc); (c) An associated dataframe (gl@other$ind.metrics) containing the individual/sample metrics (e.g. sex, latitude, longitude, etc); (d) A specimen identity field (indNames(gl)) with the unique labels applied to each individual/sample; (e) A population assignment (popNames) for each individual/specimen; (f) Flags that indicate whether or not calculable locus metrics have been updated.

This function will check to see that the genlight object conforms to expectation in regard to the above requirements, and if it does not, will rectify it.

Value

A genlight object that conforms to the expectations of dartR

Author(s)

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

Examples

x <- gl.compliance.check(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