R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Genomic Sex

set.genomic.sex

R Documentation

Genomic Sex

Description

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

Usage

 set.genomic.sex(x, chr.x = 23, chr.y = 24, plot = FALSE, 
           verbose = getOption("gaston.verbose",TRUE))

Arguments

`x`	A `bed.matrix`
`chr.x`	Id of the X chromosome (defaut value according to PLINK convention)
`chr.y`	Id of the Y chromosome (defaut value according to PLINK convention)
`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 chromsomes, 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)

Herv<c3><83><c2><a9> Perdry