MethylMix_PlotModel {MethylMix} | R Documentation

## The MethylMix_PlotModel function.

### Description

Produces plots to represent MethylMix's output.

### Usage

    MethylMix_PlotModel(GeneName, MixtureModelResults, METcancer, GEcancer = NULL,
      METnormal = NULL)

### Arguments

`GeneName` | Name of the gene for which to create a MethylMix plot.
`MixtureModelResults` | List returned by MethylMix function.
`METcancer` | Matrix with the methylation data of cancer tissue with genes in rows and samples in columns.
`GEcancer` | Gene expression data for cancer tissue with genes in rows and samples in columns (optional).
`METnormal` | Matrix with the normal methylation data of the same genes as in METcancer (optional). Again genes in rows and samples in columns.

### Value

a list with MethylMix plots, a histogram of the methylation data (MixtureModelPlot) and a scatterplot between DNA methylation and gene expression (CorrelationPlot, is NULL if gene expression data is not provided). Both plots show the different mixture components identified.

### 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)

    # Plot the most famous methylated gene for glioblastoma
    MethylMix_PlotModel("MGMT", MethylMixResults, METcancer)

    # Plot MGMT also with its normal methylation variation
    MethylMix_PlotModel("MGMT", MethylMixResults, METcancer, METnormal = METnormal)

    # Plot a MethylMix model for another gene
    MethylMix_PlotModel("ZNF217", MethylMixResults, METcancer, METnormal = METnormal)

    # Also plot the inverse correlation with gene expression (creates two separate plots)
    MethylMix_PlotModel("MGMT", MethylMixResults, METcancer, GEcancer, METnormal)

    # Plot all functional and differential genes
    for (gene in MethylMixResults$MethylationDrivers) {
         MethylMix_PlotModel(gene, MethylMixResults, METcancer, METnormal = METnormal)
    }

[Package MethylMix version 2.20.0 Index]