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| 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. |
| getCytobandSummary | extract cytoband summary from GISTIC object |
| getCytobandSummary-method | extract cytoband summary from GISTIC object |
| getFields | extract available fields from MAF object |
| getFields-method | extract available fields from MAF object |
| getGeneSummary | extract gene summary from MAF or GISTIC object |
| getGeneSummary-method | extract gene summary from MAF or GISTIC object |
| getSampleSummary | extract sample summary from MAF or GISTIC object |
| getSampleSummary-method | extract sample summary from MAF or GISTIC object |
| GISTIC | Class GISTIC |
| GISTIC-class | Class GISTIC |
| gisticPlot | 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. |
| MAF | Class MAF |
| MAF-class | Class MAF |
| mafCompare | compare two cohorts (MAF). |
| math.score | calculates MATH (Mutant-Allele Tumor Heterogeneity) score. |
| mutExclusive | Performs exact test for mutual exclusive events. |
| 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. |
| pfamDomains | pfam domain annotation and summarization. |
| plotCBSsegments | Plots segmented copy number data. |
| plotClusters | Plot density plots from clutering results. |
| plotGisticResults | Plot gistic results as a bubble plot. |
| plotmafSummary | Plots maf summary. |
| plotOncodrive | Plots results from 'oncodrive' |
| plotSignatures | Plots decomposed mutational signatures. |
| plotTiTv | Plot Transition and Trasnversion ratios. |
| plotVaf | Plots vaf distribution of genes |
| rainfallPlot | Rainfall plot to display kataegis or hyper mutated genomic regions. |
| read.maf | Read MAF files. |
| readGistic | Read and summarize gistic output. |
| subsetMaf | Subset MAF |
| titv | Classifies SNPs into transitions and transversions |
| trinucleotideMatrix | Extract single 5' and 3' bases flanking the mutated site. |
| vcr | Samll internal function to make complex events. |
| write.GisticSummary | Writes GISTIC summaries to output tab-delimited text files. |
| write.mafSummary | Writes maf summaries to output tab-delimited text files. |