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... |
generateTCGAComparePlot | Plot the comparison of the mutation load against TCGA cohorts |
generateTiTvPlot | Function to plot the frequency of Transitions and... |
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 |
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