gl.report.maf: Reports minor allele frequency (MAF) for each locus in a SNP...

In dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions

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

Description

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

Usage

gl.report.maf(
  x,
  as.pop = NULL,
  maf.limit = 0.5,
  ind.limit = 5,
  plot.display = TRUE,
  plot.theme = theme_dartR(),
  plot.colors = NULL,
  plot.dir = NULL,
  plot.file = NULL,
  bins = 25,
  verbose = NULL
)

Arguments

x	Name of the genlight object containing the SNP data [required].
as.pop	Temporarily assign another locus metric as the population for the purposes of deletions [default NULL].
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.display	Specify if plot is to be displayed in the graphics window [default TRUE].
plot.theme	User specified theme [default theme_dartR()].
plot.colors	Vector with color names for the borders and fill [default c("#2171B5", "#6BAED6")].
plot.dir	Directory to save the plot RDS files [default as specified by the global working directory or tempdir()]
plot.file	Filename (minus extension) for the RDS plot file [Required for plot save].
bins	Number of bins to display in histograms [default 25].
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.

Plot colours can be set with gl.select.colors().

If plot.file is specified, plots are saved to the directory specified by the user, or the global default working directory set by gl.set.wd() or to the tempdir().

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

Other matched report: gl.filter.excess.het(), gl.report.allna(), gl.report.callrate(), gl.report.hamming(), gl.report.locmetric(), gl.report.overshoot(), gl.report.pa(), gl.report.rdepth(), gl.report.reproducibility(), gl.report.secondaries(), gl.report.taglength()

Examples

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

dartR.base documentation built on April 4, 2025, 2:45 a.m.