GISTIC-class            Class GISTIC
MAF-class               Class MAF
annovarToMaf            Converts annovar annotations into MAF.
coOncoplot              Draw two oncoplots side by side for cohort
                        comparision.
extractSignatures       Extract mutational signatures from trinucletide
                        context.
forestPlot              Draw forest plot for differences betweeen
                        cohorts.
geneCloud               Plots wordcloud.
genesToBarcodes         Extracts Tumor Sample Barcodes where the given
                        genes are mutated.
genotypeMatrix          Creates a Genotype Matrix for every variant
getClinicalData         extract annotations from MAF object
getCytobandSummary      extract cytoband summary from GISTIC object
getFields               extract available fields from MAF object
getGeneSummary          extract gene summary from MAF or GISTIC object
getSampleSummary        extract sample summary from MAF or GISTIC
                        object
gisticBubblePlot        Plot gistic results as a bubble plot
gisticChromPlot         Plot gistic results along linearized chromosome
gisticOncoPlot          Plot gistic results.
icgcSimpleMutationToMAF
                        Converts ICGC Simple Somatic Mutation format
                        file to MAF
inferHeterogeneity      Clusters variants based on Variant Allele
                        Frequencies (VAF).
lollipopPlot            Draws lollipop plot of amino acid changes on to
                        Protein structure.
mafCompare              compare two cohorts (MAF).
mafSummary              Summary statistics of MAF
mafSurvival             Performs survival analysis
math.score              calculates MATH (Mutant-Allele Tumor
                        Heterogeneity) score.
mutCountMatrix          Generates count matrix of mutations.
oncodrive               Detect cancer driver genes based on positional
                        clustering of variants.
oncoplot                draw an oncoplot
oncostrip               draw an oncostrip similar to cBioportal
                        oncoprinter output.
oncotate                Annotates given variants using oncotator api.
pancanComparison        Perform PacCancer analysis
pfamDomains             pfam domain annotation and summarization.
plotApobecDiff          Plot differences between APOBEC enriched and
                        non-APOBEC enriched samples.
plotCBSsegments         Plots segmented copy number data.
plotClusters            Plot density plots from clutering results.
plotOncodrive           Plots results from 'oncodrive'
plotSignatures          Plots decomposed mutational signatures
plotTiTv                Plot Transition and Trasnversion ratios.
plotVaf                 Plots vaf distribution of genes
plotmafSummary          Plots maf summary.
prepareMutSig           Prepares MAF file for MutSig analysis.
rainfallPlot            Rainfall plot to display hyper mutated genomic
                        regions.
read.maf                Read MAF files.
readGistic              Read and summarize gistic output.
somaticInteractions     Exact tests to detect mutually exclusive,
                        co-occuring and altered genesets.
subsetMaf               Subset MAF
tcgaCompare             Compare mutation load against TCGA cohorts
titv                    Classifies SNPs into transitions and
                        transversions
trinucleotideMatrix     Extract single 5' and 3' bases flanking the
                        mutated site for de-novo signature analysis.
                        Also estimates APOBEC enrichment scores.
write.GisticSummary     Writes GISTIC summaries to output tab-delimited
                        text files.
write.mafSummary        Writes maf summaries to output tab-delimited
                        text files.
