compute_exome_coverage
                        Compute exome coverage from a region file
createOncoMatrix        Creates matrix for oncoplot
detectMAFGenome         A function to detect MAF genome
filterMAF               Function to filter the mutations
filter_maf_chunked      Function to filter the mutations
generateBurdenPlot      Function to generate Burden plot
generateMutationTypePlot
                        Function to generate silent and non-silent
                        mutation plot
generateOncoPlot        Function to generate a dashboard from a MAF
                        file
generateOverlapPlot     Function to generate Overlap plot
generateRibbonPlot      Function to generate a ribbon plot depicting
                        co-occurence and mutual exclusivity of gene
                        mutations
generateTCGAComparePlot
                        Plot the comparison of the mutation load
                        against TCGA cohorts
generateTiTvPlot        Function to plot the frequency of Transitions
                        and Transversions of gene mutations
generateVariantTable    Make variant table from maf file
getMAFDashboard         Function to generate a dashboard from a MAF
                        file.
getMAFdataTCGA          Function to extract the mutation data in MAF
                        format from TCGA
getTCGAClinicalAnnotation
                        Function to extract the clinical annotations
                        from TCGA
getTCGAClinicalColors   Makes reasonable colors for some TCGA clinical
                        annoations
