gl.test.heterozygosity: Tests the difference in heterozygosity between populations...

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

Tests the difference in heterozygosity between populations taken pairwise

Description

Calculates the expected heterozygosities for each population in a genlight object, and uses re-randomization to test the statistical significance of differences in heterozygosity between populations taken pairwise.

Usage

gl.test.heterozygosity(
  x,
  nreps = 100,
  alpha1 = 0.05,
  alpha2 = 0.01,
  plot.out = TRUE,
  max_plots = 6,
  plot_theme = theme_dartR(),
  plot_colors = two_colors,
  save2tmp = FALSE,
  verbose = NULL
)

Arguments

x	A genlight object containing the SNP genotypes [required].
nreps	Number of replications of the re-randomization [default 1,000].
alpha1	First significance level for comparison with diff=0 on plot [default 0.05].
alpha2	Second significance level for comparison with diff=0 on plot [default 0.01].
plot.out	If TRUE, plots a sampling distribution of the differences for each comparison [default TRUE].
max_plots	Maximum number of plots to print per page [default 6].
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 two_colors].
save2tmp	If TRUE, saves any ggplots and listings 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

Function's output

If plot.out = TRUE, plots are created showing the sampling distribution for the difference between each pair of heterozygosities, marked with the critical limits alpha1 and alpha2, the observed heterozygosity, and the zero value (if in range).

Plots and table are saved to the temporal directory (tempdir) and can be accessed with the function gl.print.reports and listed with the function gl.list.reports. Note that they can be accessed only in the current R session because tempdir is cleared each time that the R session is closed.

Examples of other themes that can be used can be consulted in

• https://ggplot2.tidyverse.org/reference/ggtheme.html and

• https://yutannihilation.github.io/allYourFigureAreBelongToUs/ggthemes/

Value

A dataframe containing population labels, heterozygosities and sample sizes

Author(s)

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

Examples

out <- gl.test.heterozygosity(platypus.gl, nreps=1, verbose=3, plot.out=TRUE)

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