GISTIC-class Class GISTIC MAF Construct an MAF object MAF-class Class MAF OncogenicPathways Enrichment of known oncogenic pathways PlotOncogenicPathways Plot oncogenic pathways 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 clinicalEnrichment Performs mutational enrichment analysis for a given clinical feature. coBarplot Draw two barplots side by side for cohort comparision. 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 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. 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. 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 plotOncodrive Plots results from 'oncodrive' 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. 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 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.