dartR: gl.subsample.loci – R documentation

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gl.subsample.loci

Subsample n loci from a genlight object and return 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 (avgPIC).

Usage

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

Arguments

`x`	– name of the genlight object containing the SNP data [required]
`n`	– number of loci to include in the subsample [required]
`method`	– "random", in which case the loci are sampled at random; or avgPIC, in which case the top n loci ranked on information content (AvgPIC) are chosen [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]

Value

A genlight object with n loci

Author(s)

Arthur Georges (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")

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