MethylMix_Predict: The MethylMix_Predict function

In gevaertlab/methylmix: MethylMix: Identifying methylation driven cancer genes

Description

Given a new data set with methylation data, this function predicts the mixture component for each new sample and driver gene. Predictions are based on posterior probabilities calculated with MethylMix'x fitted mixture model.

Usage

MethylMix_Predict(newBetaValuesMatrix, MethylMixResult)

Arguments

newBetaValuesMatrix	Matrix with new observations for prediction, genes/cpg sites in rows, samples in columns. Although this new matrix can have a different number of genes/cpg sites than the one provided as METcancer when running MethylMix, naming of genes/cpg sites should be the same.
MethylMixResult	Output object from MethylMix

Value

A matrix with predictions (indices of mixture component), driver genes in rows, new samples in columns

Examples

# load the three data sets needed for MethylMix
data(METcancer)
data(METnormal)
data(GEcancer)

# run MethylMix on a small set of example data
MethylMixResults <- MethylMix(METcancer, GEcancer, METnormal)
# toy example new data, of same dimension of original METcancer data
newMETData <- matrix(runif(length(METcancer)), nrow = nrow(METcancer))
rownames(newMETData) <- rownames(METcancer)
colnames(newMETData) <- paste0("sample", 1:ncol(METcancer))
predictions <- MethylMix_Predict(newMETData, MethylMixResults)

gevaertlab/methylmix documentation built on May 25, 2019, 5:25 p.m.