MethylMix (version 1.6.0)

MethylMix_PlotModel: Plotting a mixture model for a gene.

Description

MethylMix identifies DNA methylation driven genes by modeling DNA methylation data in cancer vs. normal and looking for homogeneous subpopulations. In addition matched gene expression data (e.g. from microarray technology or RNA sequencing) is used to identify functional DNA methylation events by requiring a negative correlation between methylation and gene expression of a particular gene.

Usage

MethylMix_PlotModel(GeneName,METdata,MixtureModelResults,MAdata=0, METnormal=0,FileName="")

Arguments

GeneName

Name of the gene for which to create a MethylMix plot.

METdata

This a matrix with the methylation data of cancer tissue with genes in rows and samples in columns

MixtureModelResults

The results object from a MethylMix run.

METnormal

This is a matrix with the normal methylation data of the same genes as in METcancer. Again genes in rows and samples in columns. The samples do not have to match with the cancer data.

MAdata

This is the matched gene expression data for the same samples as in METcancer.

FileName

Filename to export the figure. If empty figure is shown in console.

Examples

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

	# run methylmix on a small set of example data
	MethylMixResults=MethylMix(METcancer,METnormal,MAcancer)

	# Plot the most famous methylated gene for glioblastoma
	MethylMix_PlotModel('MGMT',METcancer,MethylMixResults)
	
	# plot MGMT also with its normal methylation variation
	MethylMix_PlotModel('MGMT',METcancer,MethylMixResults,MAdata=0,METnormal)

	# plot a MethylMix model for another gene
	MethylMix_PlotModel('ZNF217',METcancer,MethylMixResults,MAdata=0,METnormal)

	# also plot the inverse correlation with gene expression 
	# this creates two separate plots
	MethylMix_PlotModel('MGMT',METcancer,MethylMixResults,MAdata=MAcancer)
	
	# plot all functional and differential genes
	for (i in 1:length(MethylMixResults$MethylationDrivers)) {
     	MethylMix_PlotModel(MethylMixResults$MethylationDrivers[i],METcancer,
          MethylMixResults,MAdata=0,METnormal)
	}