Feature-based association and gene-set enrichment for copy number alteration analysis in cancer

Global functions | |
---|---|

addFeatures | Man page Source code |

addVariables | Man page Source code |

aggregateInt | Source code |

allChrs | Source code |

allCodes | Source code |

alterCodes | Source code |

alterationSummary | Man page Source code |

alterations | Source code |

calcCallFreqsInt | Source code |

calcFreqsInt | Source code |

calculateCor | Man page Source code |

checkAlter | Source code |

checkData | Source code |

checkFeatures | Source code |

checkFullModel | Source code |

checkModels | Source code |

checkSel | Source code |

checkSelCols | Source code |

checkVar | Source code |

checkVarValue | Source code |

checkYlim | Source code |

corInt | Source code |

enrichment | Source code |

facopy | Man page Source code |

facopy-package | Man page |

facopyEnrichment | Man page Source code |

facopyInfo | Man page |

facopyInfo-class | Man page |

facopyPlot | Man page Source code |

facopyPlotInt | Source code |

features | Source code |

fill | Source code |

genomes | Source code |

getAlterCodes | Source code |

getFacopyAnnot | Source code |

getFacopyInfo | Man page Source code |

getLOH | Source code |

getTypeCode | Source code |

graphPathway | Source code |

makeArmsInt | Source code |

makeCor | Source code |

makeInfo | Source code |

makeMatrixInt | Source code |

makeVars | Source code |

methods | Source code |

myCalls | Man page |

myStudy | Man page |

myVariables | Man page |

n | Source code |

ord | Source code |

pack | Source code |

plotArm | Source code |

plotBar | Man page Source code |

plotBarBps | Source code |

plotBarFeatures | Source code |

plotBarInt | Source code |

plotHist | Man page Source code |

plotPCA | Man page Source code |

plotVicinity | Source code |

plotVicinityInt | Source code |

plotZoom | Man page Source code |

preview | Man page Source code |

printList | Source code |

readCNData | Man page Source code |

readFromCNANORM | Source code |

readFromEXOMECNV | Source code |

readFromFASTCALL | Source code |

readFromFREEC | Source code |

readFromFolder | Source code |

readFromGAP | Source code |

readFromInt | Source code |

readFromONCOSNP | Source code |

readFromONCOSNPInt | Source code |

readFromONCOSNPSEQ | Source code |

readFromPATCHWORK | Source code |

readFromSEQCNA | Source code |

readFromTITAN | Source code |

refcols | Source code |

sCateg | Source code |

summary,facopyInfo-method | Man page |

summary.facopyInfo | Source code |

types | Source code |

unLOH | Source code |

variableCor | Man page Source code |

variableSummary | Man page Source code |

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