dartR (version 1.9.9.1)

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

Examples

# NOT RUN {
# 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")
# }