# Create an HTML Dashboard to Visualize Data from MAF File

## Documentation for package ‘MAFDash’ version 0.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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