Subsamples n loci from a genlight object and return it as a genlight object
Source:R/gl.subsample.loci.r
gl.subsample.loci.Rd
This is a support script, to subsample a genlight {adegenet} object based on loci. Two methods are used to subsample, random and based on information content.
Arguments
- x
Name of the genlight object containing the SNP or presence/absence (SilicoDArT) data [required].
- n
Number of loci to include in the subsample [required].
- method
Method: 'random', in which case the loci are sampled at random; or 'pic', in which case the top n loci ranked on information content are chosen. Information content is stored in AvgPIC in the case of SNP data and in PIC in the the case of presence/absence (SilicoDArT) data [default 'random'].
- mono.rm
Delete monomorphic loci before sampling [default FALSE].
- 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].
Author
Custodian: Luis Mijangos – Post to https://groups.google.com/d/forum/dartr
Examples
# SNP data
gl2 <- gl.subsample.loci(testset.gl, n=200, method='pic')
#> Starting gl.subsample.loci
#> Processing genlight object with SNP data
#> Warning: Dataset contains monomorphic loci which will be included in the gl.subsample.loci selections
#> Completed: gl.subsample.loci
#>
# Tag P/A data
gl2 <- gl.subsample.loci(testset.gl, n=100, method='random')
#> Starting gl.subsample.loci
#> Processing genlight object with SNP data
#> Warning: Dataset contains monomorphic loci which will be included in the gl.subsample.loci selections
#> Subsampling at random 100 loci from genlight object
#> Completed: gl.subsample.loci
#>