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

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].

Value

A genlight object that conforms to the expectations of dartR

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.

Author

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

Examples

x <- gl.compliance.check(testset.gl)
#> Starting gl.compliance.check 
#>   Processing genlight object with SNP data
#>   Checking coding of SNPs
#>     SNP data scored NA, 0, 1 or 2 confirmed
#>   Checking locus metrics and flags
#>   Recalculating locus metrics
#>   Checking for monomorphic loci
#>     Dataset contains monomorphic loci
#>   Checking for loci with all missing data
#>     No loci with all missing data detected
#>   Checking whether individual names are unique.
#>   Checking for individual metrics
#>     Individual metrics confirmed
#>   Checking for population assignments
#>     Population assignments confirmed
#>   Spelling of coordinates checked and changed if necessary to 
#>             lat/lon
#> Completed: gl.compliance.check 
#> 
x <- gl.compliance.check(testset.gs)
#> Starting gl.compliance.check 
#>   Processing genlight object with Presence/Absence (SilicoDArT) data
#>   Checking coding of Tag P/A data
#>     Tag P/A data (SilicoDArT) scored 1, 0 (present or 
#>                         absent) confirmed
#>   Checking locus metrics and flags
#>   Recalculating locus metrics
#>   Checking for monomorphic loci
#>     Dataset contains monomorphic loci
#>   Checking for loci with all missing data
#>     No loci with all missing data detected
#>   Checking whether individual names are unique.
#>   Checking for individual metrics
#>     Individual metrics confirmed
#>   Checking for population assignments
#>     Population assignments confirmed
#>   Spelling of coordinates checked and changed if necessary to 
#>             lat/lon
#> Completed: gl.compliance.check 
#>