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