Function reference • MAFDash

All functions
`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
`filterMAF2()`	Function to filter the mutations
`generateBurdenPlot()`	Function to generate Burden plot
`generateCOSMICMutSigSimHeatmap()`	Computes and plot the cosine similarity of each individual signature is computed against each COSMIC signature from COMIC V3.2
`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

Reference