API for benilton/crlmm
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
| Global functions | |
|---|---|
| .close | Source code |
| .onAttach | Source code |
| .onUnload | Source code |
| .open | Source code |
| .posterior | Source code |
| .test | Source code |
| ABpanel | Man page Source code |
| ACN | Source code |
| AddBackNoVarianceSNPs | Source code |
| BafLrrSetList | Man page |
| BafLrrSetList,CNSet-method | Man page |
| C1 | Source code |
| C2 | Source code |
| C3 | Source code |
| CA | Man page |
| CA,CNSet-method | Man page |
| CB | Man page |
| CB,CNSet-method | Man page |
| Ns | Man page |
| Ns,AssayData-method | Man page |
| Ns,CNSet-method | Man page |
| OligoSetList | Man page |
| OligoSetList,CNSet-method | Man page |
| PredictionRegion-class | Man page |
| [,PredictionRegion,ANY,ANY,ANY-method | Man page |
| affyCdfNames | Source code |
| assignCalls | Source code |
| assignCalls1Cluster | Source code |
| assignCalls2Cluster | Source code |
| assignCalls3Cluster | Source code |
| assignCallsOneSNP | Source code |
| calculateKrlmmCoefficients | Source code |
| calculateMahalDist1Cluster | Source code |
| calculateMahalDist2Cluster | Source code |
| calculateMahalDist3Cluster | Source code |
| calculateOneParams1Cluster | Source code |
| calculateOneParams2Cluster | Source code |
| calculateOneParams3Cluster | Source code |
| calculateParameters | Source code |
| calculateParameters1Cluster | Source code |
| calculateParameters2Cluster | Source code |
| calculateParameters3Cluster | Source code |
| calculatePriorValues | Source code |
| calculatePriorcentersC | Source code |
| calculateRBaf | Man page |
| calculateRBaf,CNSet-method | Man page |
| calculateRBafCNSet | Source code |
| calculateRTheta | Source code |
| celDates | Man page Source code |
| changeToCrlmmAnnotationName | Source code |
| checkNumberOfSNPs | Source code |
| cleancdfname | Source code |
| cnSetExample | Man page |
| cnSetExample2 | Man page |
| cnrma2 | Source code |
| cnrmaAffy | Man page Source code |
| coerce,CNSet,oligoSnpSet-method | Man page |
| computeAverageLogIntensity | Source code |
| computeCallPr | Source code |
| computeLogRatio | Source code |
| construct | Source code |
| constructAffyCNSet | Man page Source code |
| constructBafLrrSetListFrom | Source code |
| constructIlluminaAssayData | Source code |
| constructIlluminaCNSet | Source code |
| constructIlluminaFeatureData | Source code |
| constructInf | Man page Source code |
| constructOligoSetListFrom | Source code |
| corr | Man page |
| corr,AssayData-method | Man page |
| corr,CNSet-method | Man page |
| crlmm | Man page Source code |
| crlmm-package | Man page |
| crlmm2 | Man page Source code |
| crlmmCopynumber | Man page Source code |
| crlmmCopynumber2 | Man page Source code |
| crlmmCopynumberLD | Man page |
| crlmmGT | Source code |
| crlmmGT2 | Source code |
| crlmmIllumina | Man page |
| dbvn | Source code |
| dqrlsWrapper | Source code |
| ellipseCenters | Source code |
| estimateCnParameters | Source code |
| fit.lm1 | Source code |
| fit.lm2 | Source code |
| fit.lm3 | Source code |
| fit.lm4 | Source code |
| fit.wls | Source code |
| fitAffySnpMixture56 | Source code |
| genotype | Man page Source code |
| genotype.Illumina | Man page Source code |
| genotype2 | Man page Source code |
| genotypeAffy | Man page Source code |
| genotypeCorrelation | Source code |
| genotypeInf | Man page Source code |
| genotypeLD | Man page |
| genotypeSummary | Source code |
| genotypes | Man page Source code |
| getAvailableIlluminaGenomeBuild | Source code |
| getBAF | Source code |
| getCor | Source code |
| getCrlmmAnnotationName | Source code |
| getFeatureData | Source code |
| getKrlmmVGLMCoefficients | Source code |
| getMedians | Source code |
| getNumberOfCores | Source code |
| getNumberOfSNPs | Source code |
| getNumberOfSamples | Source code |
| getProtocolData.Affy | Source code |
| getProtocolData.Illumina | Source code |
| getSigma2 | Source code |
| getTau2 | Source code |
| getVar | Source code |
| getVarInEnv | Source code |
| gtypeCallerR | Source code |
| gtypeCallerR2 | Source code |
| hardyweinberg | Source code |
| illuminaCdfNames | Source code |
| imputeAA | Source code |
| imputeAA.AB | Source code |
| imputeAB.BB | Source code |
| imputeAcrossBatch | Source code |
| imputeBB | Source code |
| imputeCenter | Source code |
| imputeCenterX | Source code |
| imputeCentersForMonomorphicSnps | Source code |
| imputeGender | Source code |
| indexComplete | Source code |
| intMedianSummaries | Source code |
| isCall | Source code |
| isLoaded | Source code |
| isPackageLoaded | Source code |
| isValidCdfName | Source code |
| krlmm | Source code |
| krlmmImputeGender | Source code |
| krlmmnopkg | Source code |
| linearParamElementReplace | Source code |
| lines,CNSet-method | Man page |
| list2SnpSet | Source code |
| loadObject | Source code |
| loader | Source code |
| loessnormalization | Source code |
| mads | Man page |
| mads,AssayData-method | Man page |
| mads,CNSet-method | Man page |
| medianSummaries | Source code |
| medians | Man page |
| medians,AssayData-method | Man page |
| medians,CNSet-method | Man page |
| nuA | Man page |
| nuA,CNSet-method | Man page |
| nuB | Man page |
| nuB,CNSet-method | Man page |
| numberGenotypes | Source code |
| paramNames | Source code |
| phiA | Man page |
| phiA,CNSet-method | Man page |
| phiB | Man page |
| phiB,CNSet-method | Man page |
| plotSNPs | Man page Source code |
| plotSamples | Man page Source code |
| posteriorMean.snp | Source code |
| posteriorProbability | Man page |
| posteriorProbability,CNSet-method | Man page |
| predictKwithVGLM | Source code |
| predictionRegion | Man page |
| predictionRegion,CNSet,integer-method | Man page |
| preprocessInf | Man page Source code |
| preprocessInfinium2 | Source code |
| processCEL | Source code |
| processIDAT | Source code |
| processOneGenCallFile | Source code |
| quantilenormalization | Source code |
| rawCopynumber | Man page |
| rawCopynumber,CNSet-method | Man page |
| readGenCallOutput | Man page Source code |
| readIdatFiles | Man page Source code |
| readIdatFiles2 | Man page |
| rowCors | Source code |
| rowCovs | Source code |
| rowMAD | Source code |
| shrink | Source code |
| shrinkGenotypeSummaries | Source code |
| shrinkSummary | Source code |
| snprma | Man page Source code |
| snprma2 | Man page Source code |
| snprmaAffy | Man page Source code |
| stripNormalize | Source code |
| stupidSplineBasis | Source code |
| sum.mymatrix | Source code |
| summarizeMaleXNps | Source code |
| summarizeNps | Source code |
| summarizeSnps | Source code |
| summarizeXGenotypes | Source code |
| tau2 | Man page |
| tau2,AssayData-method | Man page |
| tau2,CNSet-method | Man page |
| totalCopynumber | Man page |
| totalCopynumber,CNSet-method | Man page |
| validCEL | Man page Source code |
| validCdfNames | Man page Source code |
| verifyChrXSNPs | Source code |
| verifyChrYSNPs | Source code |
| whichMarkers | Source code |
| whichPlatform | Source code |
| xyplot | Man page |
| xyplot,formula,CNSet-method | Man page |
