predictSex: Sex Prediction of samples assayed on the Illumina Infinium...
In wateRmelon: Illumina 450 methylation array normalization and metrics

Description Usage Arguments Details Value Author(s)

Predicts the sex of samples

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

`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

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.

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

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

wateRmelon documentation built on Nov. 8, 2020, 7:47 p.m.