gl.report.maf {dartR}

Reports minor allele frequency (MAF) for each locus in a SNP dataset

Description

This script provides summary histograms of MAF for each population in the dataset and an overall histogram to assist the decision of choosing thresholds for the filter function gl.filter.maf

Usage

gl.report.maf(
  x,
  maf.limit = 0.5,
  ind.limit = 5,
  plot.out = TRUE,
  plot_theme = theme_dartR(),
  plot_colors_pop = discrete_palette,
  plot_colors_all = two_colors,
  bins = 25,
  save2tmp = FALSE,
  verbose = NULL
)

Arguments

x

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

maf.limit

Show histograms MAF range <= maf.limit [default 0.5].

ind.limit

Show histograms only for populations of size greater than ind.limit [default 5].

plot.out

Specify if plot is to be produced [default TRUE].

plot_theme

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

plot_colors_pop

A color palette for population plots [default discrete_palette].

plot_colors_all

List of two color names for the borders and fill of the overall plot [default two_colors].

bins

Number of bins to display in histograms [default 25].

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

The function gl.filter.maf will filter out the loci with MAF below a specified threshold.

Function's output

The minimum, maximum, mean and a tabulation of MAF quantiles against thresholds rate are provided. Output also includes a boxplot and a histogram.

This function reports the MAF for each of several quantiles. Quantiles are partitions of a finite set of values into q subsets of (nearly) equal sizes. In this function q = 20. Quantiles are useful measures because they are less susceptible to long-tailed distributions and outliers.

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

An unaltered genlight object

Author(s)

Custodian: Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

See Also

gl.filter.maf, gl.list.reports, gl.print.reports

Other report functions: gl.report.bases(), gl.report.callrate(), gl.report.diversity(), gl.report.hamming(), gl.report.heterozygosity(), gl.report.hwe(), gl.report.ld.map(), gl.report.locmetric(), gl.report.monomorphs(), gl.report.overshoot(), gl.report.parent.offspring(), gl.report.pa(), gl.report.rdepth(), gl.report.reproducibility(), gl.report.secondaries(), gl.report.sexlinked(), gl.report.taglength()

Examples

gl <- gl.report.maf(platypus.gl)