gl.random.snp: Randomly changes the allocation of 0's and 2's in a genlight...

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Randomly changes the allocation of 0's and 2's in a genlight object

Description

This function samples randomly half of the SNPs and re-codes, in the sampled SNP's, 0's by 2's.

Usage

gl.random.snp(x, plot.out = TRUE, save2tmp = FALSE, verbose = NULL)

Arguments

x	Name of the genlight object containing the SNP data [required].
plot.out	Specify if a plot is to be produced [default TRUE].
save2tmp	If TRUE, saves any ggplots to the session temporary directory (tempdir) [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 NULL, unless specified using gl.set.verbosity].

Details

DArT calls the most common allele as the reference allele. In a genlight object, homozygous for the reference allele are coded with a '0' and homozygous for the alternative allele are coded with a '2'. This causes some distortions in visuals from time to time.

If plot.out = TRUE, two smear plots (pre-randomisation and post-randomisation) are presented using a random subset of individuals (10) and loci (100) to provide an overview of the changes.

Resultant ggplots are saved to the session's temporary directory.

Value

Returns a genlight object with half of the loci re-coded.

Author(s)

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

Examples

require("dartR.data")
res <- gl.random.snp(platypus.gl[1:5,1:5],verbose = 5)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.