MethylMix_Predict {MethylMix} | R Documentation

## The MethylMix_Predict function

### 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)

[Package MethylMix version 2.20.0 Index]