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| annovarToMaf | Converts annovar annotations into MAF. |
| clinicalEnrichment | Performs mutational enrichment analysis for a given clinical feature. |
| coBarplot | Draw two barplots side by side for cohort comparision. |
| compareSignatures | Compares identified denovo mutational signatures to known COSMIC signatures |
| coOncoplot | Draw two oncoplots side by side for cohort comparision. |
| drugInteractions | Drug-Gene Interactions |
| estimateSignatures | Estimate number of signatures based on cophenetic correlation metric |
| extractSignatures | Extract mutational signatures from trinucleotide context. |
| 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 |
| getClinicalData-method | extract annotations from MAF object |
| 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 |
| 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). |
| intersectMAF | Set Operations for MAF objects |
| lollipopPlot | Draws lollipop plot of amino acid changes on to Protein structure. |
| lollipopPlot2 | Compare two lollipop plots |
| MAF | Class MAF |
| MAF-class | Class MAF |
| mafCompare | compare two cohorts (MAF). |
| mafSummary | Summary statistics of MAF |
| mafSurvGroup | Performs survival analysis for a geneset |
| mafSurvival | Performs survival analysis |
| 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. |
| OncogenicPathways | Enrichment of known oncogenic pathways |
| 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 |
| plotmafSummary | Plots maf summary. |
| plotOncodrive | Plots results from 'oncodrive' |
| PlotOncogenicPathways | Plot oncogenic pathways |
| plotSignatures | Plots decomposed mutational signatures |
| plotTiTv | Plot Transition and Trasnversion ratios. |
| plotVaf | Plots vaf distribution of genes |
| 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. |
| 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 |
| tcgaCompare | Compare mutation load against TCGA cohorts |
| tcgaDriverBP | Compare genes to known TCGA drivers and their biological pathways |
| 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. |