Description Usage Arguments Details Value Author(s)
Predicts the sex of samples
1 |
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>
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