gl.compliance.check: Checks a genlight object to see if it complies with dartR...

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

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

Description

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

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

1. The SNP genotypes or Tag Presence/Absence data (SilicoDArT);

2. An associated dataframe (gl@other$loc.metrics) containing the locus metrics (e.g. Call Rate, Repeatability, etc);

3. An associated dataframe (gl@other$ind.metrics) containing the individual/sample metrics (e.g. sex, latitude (=lat), longitude(=lon), etc);

4. A specimen identity field (indNames(gl)) with the unique labels applied to each individual/sample;

5. A population assignment (popNames) for each individual/specimen;

6. Flags that indicate whether or not calculable locus metrics have been updated.

Value

A genlight object that conforms to the expectations of dartR

Author(s)

Custodian: Luis Mijangos – Post to https://groups.google.com/d/forum/dartr

Examples

x <- gl.compliance.check(testset.gl)
x <- gl.compliance.check(testset.gs)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.