set.genomic.sex: Genomic Sex

In gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

Genomic Sex

Description

Returns an updated bed.matrix with a new variable for the genomic sex of each individual.

Usage

 set.genomic.sex(x, plot = FALSE, verbose = getOption("gaston.verbose",TRUE)) 

Arguments

x	A bed.matrix
plot	If TRUE, plots the variables used for the clustering
verbose	If TRUE, displays information on the function actions

Details

For each individual, the function uses the hetorozygosity rate for SNPs on X chromosome, and the call rate for SNPs on the Y chromosomes (both statistics computed by set.stats), to cluster the individuals using kmeans.

If plot = TRUE, a plot is produced with the two variables used and the clusters determined by kmeans.

Value

A bed.matrix similar to x, with a new variable x@ped$genomic.sex containing the genomic sex for each individual.

Author(s)

Hervé Perdry

See Also

set.stats, set.hwe

gaston documentation built on May 29, 2024, 7:33 a.m.