predictSex {wateRmelon} | R Documentation

## Sex Prediction of samples assayed on the Illumina Infinium BeadChip platform

### Description

Predicts the sex of samples

### Usage

    predictSex(x, x.probes, pc = 2, plot=TRUE, irlba=TRUE, center=FALSE, scale. = FALSE)

### Arguments

`x` | A matrix containing values equivalent to betas. Can be the full set of CpG features or pre-filtered for X-chromosomes.
`x.probes` | Default NULL, assuming that x is a beta matrix consisting of only X-chromosome probes, otherwise supply with vector containing logical or numeric index of probes on the X-chromosome.
`pc` | The principal component to guess sex across (usually the 2nd one in most cases)
`plot` | Logical, indicated whether or not to plot the prediction
`irlba` | Logical, indicate whether or not to use the faster method to generate principal components
`center` | Logical, indicate whether or not to center data around 0
`scale.` | Logical, indicate whether or not to scale data prior to prcomp

### Details

Function attempts to predictSex based on the colMeans of the X chromsome and princpal components. Assumes that there are two sexes to predict and as a result will perform poorly on data-sets consisting of a single sex.

### Value

Character Vector of predicted sex for each sample, samples that were not guess are assigned 'Unknown'

### Author(s)

Tyler J. Gorrie-Stone Who to contact: <tgorri@essex.ac.uk>

[Package wateRmelon version 1.28.0 Index]