Man pages for MAFDash
Create an HTML Dashboard to Visualize Data from MAF File

compute_exome_coverageCompute exome coverage from a region file
createOncoMatrixCreates matrix for oncoplot
detectMAFGenomeA function to detect MAF genome
filterMAFFunction to filter the mutations
filter_maf_chunkedFunction to filter the mutations
generateBurdenPlotFunction to generate Burden plot
generateMutationTypePlotFunction to generate silent and non-silent mutation plot
generateOncoPlotFunction to generate a dashboard from a MAF file
generateOverlapPlotFunction to generate Overlap plot
generateRibbonPlotFunction to generate a ribbon plot depicting co-occurence and...
generateTCGAComparePlotPlot the comparison of the mutation load against TCGA cohorts
generateTiTvPlotFunction to plot the frequency of Transitions and...
generateVariantTableMake variant table from maf file
getMAFDashboardFunction to generate a dashboard from a MAF file.
getMAFdataTCGAFunction to extract the mutation data in MAF format from TCGA
getTCGAClinicalAnnotationFunction to extract the clinical annotations from TCGA
getTCGAClinicalColorsMakes reasonable colors for some TCGA clinical annoations
MAFDash documentation built on April 1, 2022, 9:05 a.m.