GISTIC-class            Class GISTIC
MAF                     Construct an MAF object
MAF-class               Class MAF
annovarToMaf            Converts annovar annotations into MAF.
bamreadcounts           extract nucleotide counts for targeted variants
                        from the BAM file.
cancerhotspots          Genotype known cancer hotspots from the tumor
                        BAM file
cancerhotspotsAggr      Aggregate cancerhotspots reports
clinicalEnrichment      Performs mutational enrichment analysis for a
                        given clinical feature.
coBarplot               Draw two barplots side by side for cohort
                        comparision.
coGisticChromPlot       Co-plot version of gisticChromPlot()
coOncoplot              Draw two oncoplots side by side for cohort
                        comparision.
compareSignatures       Compares identified denovo mutational
                        signatures to known COSMIC signatures
drugInteractions        Drug-Gene Interactions
estimateSignatures      Estimate number of signatures based on
                        cophenetic correlation metric
extractSignatures       Extract mutational signatures from
                        trinucleotide context.
filterMaf               Filter MAF objects
forestPlot              Draw forest plot for differences betweeen
                        cohorts.
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
gisticCompare           compare two GISTIC objects
gisticOncoPlot          Plot gistic results.
gtMarkers               Extract read counts from genetic markers for
                        ASCAT analysis
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.
lollipopPlot2           Compare two lollipop plots
maf2mae                 Convert MAF to MultiAssayExperiment object
mafCompare              compare two cohorts (MAF).
mafSummary              Summary statistics of MAF
mafSurvGroup            Performs survival analysis for a geneset
mafSurvival             Performs survival analysis
mafbarplot              Creates a bar plot
math.score              calculates MATH (Mutant-Allele Tumor
                        Heterogeneity) score.
merge_mafs              Merge multiple mafs into single MAF
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.
pathways                Enrichment of known oncogenic or custom
                        pathways
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.
plotCophenetic          Draw an elbow plot of cophenetic correlation
                        metric.
plotEnrichmentResults   Plots results from clinicalEnrichment analysis
plotMosdepth            Plot results from mosdepth output for
                        Tumor/Normal pair
plotMosdepth_t          Plot results from mosdepth output
plotOncodrive           Plots results from 'oncodrive'
plotPathways            Plot oncogenic pathways
plotProtein             Display protein domains
plotSignatures          Plots decomposed mutational signatures
plotTiTv                Plot Transition and Trasnversion ratios.
plotVaf                 Plots vaf distribution of genes
plotmafSummary          Plots maf summary.
prepAscat               Prepare input files for ASCAT
prepAscat_t             Prepare input files for ASCAT tumor only
                        samples
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.
sampleSwaps             Identify sample swaps and similarities
segSummarize            Summarize CBS segmentation results
segmentLogR             Segment and plot log ratio values with DNACopy
setdiffMAF              Set Operations for MAF objects
signatureEnrichment     Performs sample stratification based on
                        signature contribution and enrichment analysis.
somaticInteractions     Exact tests to detect mutually exclusive,
                        co-occuring and altered genesets.
subsetMaf               Subset MAF objects
survGroup               Predict genesets associated with survival
tcgaAvailable           Prints available TCGA datasets
tcgaCompare             Compare mutation load against TCGA cohorts
tcgaDriverBP            Compare genes to known TCGA drivers and their
                        biological pathways
tcgaLoad                Loads a TCGA cohort
titv                    Classifies SNPs into transitions and
                        transversions
tmb                     Estimate Tumor Mutation Burden
trinucleotideMatrix     Extract single 5' and 3' bases flanking the
                        mutated site for de-novo signature analysis.
                        Also estimates APOBEC enrichment scores.
vafCompare              compare VAF across two cohorts
write.GisticSummary     Writes GISTIC summaries to output tab-delimited
                        text files.
write.mafSummary        Writes maf summaries to output tab-delimited
                        text files.
