gl.drop.sexlinked {dartR.sexlinked}

Removes loci that are sex linked

Description

This function identifies sex-linked and autosomal loci present in a SNP dataset (genlight object) using individuals with known sex. It identifies five types of loci: w-linked or y-linked, sex-biased, z-linked or x-linked, gametologous and autosomal.

This function produces as output a genlight object with autosomal loci only.

Usage

gl.drop.sexlinked(
  x,
  system = NULL,
  ncores = 1,
  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. This genlight object needs to contain the sex of the individuals. See explanation in details [required].

system

String that declares the sex-determination system of the species: 'zw' or 'xy' [required].

ncores

Number of processes to be used in parallel operation. If ncores > 1 parallel operation is activated, see "Details" section [default 1].

plot.display

Creates four output plots. See explanation in details [default TRUE].

plot.theme

Theme for the plot. See Details for options [default theme_dartR()].[not yet implemented]

plot.colors

[not implemented yet]

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

The genlight object must contain in gl@other$ind.metrics a column named "id", and a column named "sex" in which individuals with known-sex are assigned 'M' for male, or 'F' for female. The function ignores individuals that are assigned anything else or nothing at all (unknown-sex).

The creation of plots can be turned-off (plot.display = FALSE) in order to save a little bit of running time for very large datasets (>50,000 SNPs). However, we strongly encourage you to always inspect the output plots at least once to make sure everything is working properly.

Function's output

This function returns as output a genlight object that contains only autosomal loci (i.e. sex-linked loci have been dropped.)

And four plots:

• A BEFORE plot based on loci call rate by sex, with w/y-linked loci colored in yellow and sex-biased loci in blue

• An AFTER plot based on loci call rate by sex, with sex-linked loci removed

• A BEFORE plot based on loci heterozygosity by sex, with z/x-linked loci colored in orange and gametologs in green

• An AFTER plot based on loci heterozygosity by sex, with sex-linked loci removed

Value

A genlight object and 4 plots.

Author(s)

Custodian: Diana Robledo-Ruiz – Post to https://groups.google.com/d/forum/dartr

References

• Robledo‐Ruiz, D. A., Austin, L., Amos, J. N., Castrejón‐Figueroa, J., Harley, D. K., Magrath, M. J., Sunnucks, P., & Pavlova, A. (2023). Easy‐to‐use R functions to separate reduced‐representation genomic datasets into sex‐linked and autosomal loci, and conduct sex assignment. Molecular Ecology Resources, 00, 1-21.

Examples

LBP_noSexLinked <- gl.drop.sexlinked(x = LBP, system = "xy", plot.display = TRUE, ncores = 1)
LBP_noSexLinked