gl.report.sexlinked: Filters loci that are sex linked

In dartR.sexlinked: Analysing SNP Data to Identify Sex-Linked Markers

Filters 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 dataframe and 2 plots.

Usage

gl.report.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 two 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 two plots:

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

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

And a dataframe in which loci are in rows, and columns:

• index - Index number to identify loci

• count.F.miss - Count of females that have this locus as missing data (NA).

• count.M.miss - Count of males that have this locus as missing data (NA)

• count.F.scored - Count of females that have this locus scored (0, 1 or 2; i.e. non-missing)

• count.M.scored - Count of males that have this locus scored (0, 1 or 2; i.e. non-missing)

• ratio - Fisher's exact test estimate testing for the independence of call rate and sex for this locus

• p.value - P-value for the Fisher's exact test estimate

• p.adjusted - P-value adjusted for false discovery rate

• scoringRate.F - Female call rate (proportion of females that were scored for this locus; x-axis in the 1st plot)

• scoringRate.M - Male call rate (proportion of males that were scored for this locus; y-axis in the 1st plot)

• w.linked/y.linked - Boolean for this locus being w-linked/y-linked

• sex.biased - Boolean for this locus having sex-biased call rate

• count.F.het - Count of females that are heterozygous for this locus

• count.M.het - Count of males that are heterozygous for this locus

• count.F.hom - Count of females that are homozygous for this locus

• count.M.hom - Count of males that are homozygous for this locus

• stat - Fisher's exact test estimate testing for the independence of heterozygosity and sex for this locus

• stat.p.value - P-value for the Fisher's exact test estimate

• stat.p.adjusted - P-value adjusted for false discovery rate

• heterozygosity.F - Proportion of females that are heterozygotes for this locus (x-axis in the 2nd plot)

• heterozygosity.M - Proportion of males that are heterozygotes for this locus (y-axis in the 2nd plot)

• z.linked/x.linked - Boolean for this locus being z-linked/x.linked

• gametolog - Boolean for this locus being a gametolog

Value

A dataframe and 2 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

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

dartR.sexlinked documentation built on June 24, 2024, 5:07 p.m.