API for PoisonAlien/maftools
Summarize, Analyze and Visualize MAF Files
| Global functions | |
|---|---|
| .dnaCopy_plotter | Source code |
| FUN | Source code Source code |
| GISTIC | Man page |
| GISTIC-class | Man page |
| MAF | Man page Source code |
| MAF-class | Man page |
| add_oncoprint | Source code |
| add_oncoprint2 | Source code |
| annovarToMaf | Man page Source code |
| bamreadcounts | Man page Source code |
| binconf | Source code |
| cancerhotspots | Man page Source code |
| cancerhotspotsAggr | Man page Source code |
| clinicalEnrichment | Man page Source code |
| coBarplot | Man page Source code |
| coGisticChromPlot | Man page Source code |
| coOncoplot | Man page Source code |
| compareSignatures | Man page Source code |
| createOncoMatrix | Source code |
| dashboard | Source code |
| detect_kataegis_chr | Source code |
| dirichletClusters | Source code |
| drugInteractions | Man page Source code |
| estimateSignatures | Man page Source code |
| estimate_binconf | Source code |
| extractSignatures | Man page Source code |
| filterCopyNumber | Source code |
| filterMaf | Man page Source code |
| fisherCorrection | Source code |
| forestPlot | Man page Source code |
| genesToBarcodes | Man page Source code |
| genotypeMatrix | Man page Source code |
| getClinicalData | Man page |
| getClinicalData,MAF-method | Man page |
| getCytobandSummary | Man page |
| getCytobandSummary,GISTIC-method | Man page |
| getFields | Man page |
| getFields,MAF-method | Man page |
| getGeneSummary | Man page |
| getGeneSummary,GISTIC-method | Man page |
| getGeneSummary,MAF-method | Man page |
| getSampleSummary | Man page |
| getSampleSummary,GISTIC-method | Man page |
| getSampleSummary,MAF-method | Man page |
| get_lp_data | Source code |
| get_m12_annotation_colors | Source code |
| get_threshold | Source code |
| gisticBubblePlot | Man page Source code |
| gisticChromPlot | Man page Source code |
| gisticCompare | Man page Source code |
| gisticOncoPlot | Man page Source code |
| gtMarkers | Man page Source code |
| icgcSimpleMutationToMAF | Man page Source code |
| inferHeterogeneity | Man page Source code |
| intersectMAF | Man page |
| layoutMain | Source code |
| layoutcol | Source code |
| layoutrow | Source code |
| leftover | Source code |
| leftovercol | Source code |
| leftoverrow | Source code |
| lollipopPlot | Man page Source code |
| lollipopPlot2 | Man page Source code |
| maf2mae | Man page Source code |
| mafCompare | Man page Source code |
| mafSummary | Man page Source code |
| mafSurvGroup | Man page Source code |
| mafSurvival | Man page Source code |
| mafbarplot | Man page Source code |
| mapMutsToSegs | Source code |
| math.score | Man page Source code |
| merge_mafs | Man page Source code |
| mutCountMatrix | Man page Source code |
| normalize_sizes | Source code |
| oncodrive | Man page Source code |
| oncoplot | Man page Source code |
| oncostrip | Man page Source code |
| pad_rectangle | Source code |
| padded_squarify | Source code |
| parse_prot | Source code |
| pathways | Man page Source code |
| pfamDomains | Man page Source code |
| plotApobecDiff | Man page Source code |
| plotCBSsegments | Man page Source code |
| plotClusters | Man page Source code |
| plotCophenetic | Man page Source code |
| plotEnrichmentResults | Man page Source code |
| plotMosdepth | Man page Source code |
| plotMosdepth_t | Man page Source code |
| plotOncodrive | Man page Source code |
| plotPathways | Man page Source code Source code |
| plotProtein | Man page Source code |
| plotSignatures | Man page Source code |
| plotTiTv | Man page Source code |
| plotVaf | Man page Source code |
| plotmafSummary | Man page Source code |
| prepAscat | Man page Source code |
| prepAscat_t | Man page Source code |
| prepareMutSig | Man page Source code |
| print_mat | Source code |
| rainfallPlot | Man page Source code |
| read.maf | Man page Source code |
| readGistic | Man page Source code |
| readSegs | Source code |
| refineClusters | Source code |
| repelPoints | Source code |
| run_surv | Source code |
| sampleSwaps | Man page Source code |
| segSummarize | Man page Source code |
| segmentLogR | Man page Source code |
| setdiffMAF | Man page Source code |
| shiftPoints | Source code |
| signatureEnrichment | Man page Source code |
| somaticInteractions | Man page Source code |
| squarify | Source code |
| subsetMaf | Man page Source code |
| summarizeGistic | Source code |
| summarizeMaf | Source code |
| survGroup | Man page Source code |
| tcgaAvailable | Man page Source code |
| tcgaCompare | Man page Source code |
| tcgaDriverBP | Man page Source code |
| tcgaLoad | Man page Source code |
| titv | Man page Source code |
| tmb | Man page Source code |
| trinucleotideMatrix | Man page Source code |
| vafCompare | Man page Source code |
| validateMaf | Source code |
| worst_ratio | Source code |
| write.GisticSummary | Man page Source code |
| write.mafSummary | Man page Source code |
