gl.randomize.snps {dartR.base}

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.

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

Usage

gl.randomize.snps(
  x,
  plot.display = TRUE,
  plot.theme = theme_dartR(),
  plot.colors = NULL,
  plot.file = NULL,
  plot.dir = NULL,
  verbose = NULL
)

gl.randomize.snps(
  x,
  plot.display = TRUE,
  plot.theme = theme_dartR(),
  plot.colors = NULL,
  plot.file = NULL,
  plot.dir = NULL,
  verbose = NULL
)

Arguments

x

Name of the genlight object containing the SNP data [required].

plot.display

If TRUE, resultant plots are displayed in the plot window [default TRUE].

plot.theme

Theme for the plot. See Details for options [default theme_dartR()].

plot.colors

List of two color names for the borders and fill of the plots [default c("#2171B5","#6BAED6")].

plot.file

Name for the RDS binary file to save (base name only, exclude extension) [default NULL]

plot.dir

Directory to save the plot RDS files [default as specified by the global working directory or tempdir()]

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.display = 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.

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.display = 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.

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.randomize.snps(platypus.gl[1:5,1:5],verbose = 5)
gl <- gl.filter.monomorphs(testset.gl)
res <- gl.randomize.snps(gl,verbose = 5)