Create an HTML Dashboard to Visualize Data from MAF File


[Up] [Top]

Documentation for package ‘MAFDash’ version 0.2.1

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