dartR.base (version 1.0.5)

gl.subsample.loci: Subsamples n loci from a genlight object and return it as a genlight object

Description

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.

Usage

gl.subsample.loci(x, n, method = "random", mono.rm = FALSE, verbose = NULL)

Value

A genlight object with n loci

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')
# Tag P/A data
  gl2 <- gl.subsample.loci(testset.gl, n=100, method='random')