API for MultiPhen
A Package to Test for Multi-Trait Association
| Global functions | |
|---|---|
| .abf | Source code |
| .abfSig | Source code |
| .allFreq | Source code |
| .applySidakCorrection | Source code |
| .applyTrans | Source code |
| .as.numeric1 | Source code |
| .backwardSelection | Source code |
| .bafratio | Source code Source code |
| .calcExpectedGeno | Source code |
| .calcOffset | Source code |
| .calcPPA | Source code |
| .centralise | Source code |
| .chol | Source code |
| .cholesky | Source code |
| .closeGenoConnection | Source code |
| .cnt | Source code |
| .cntNa | Source code |
| .cntVec | Source code |
| .cnvdistr | Source code |
| .convAvgToUnc | Source code |
| .convAvgToUncM | Source code |
| .convAvgToUncMat | Source code |
| .convertFactorToMatrix | Source code |
| .convertMatrixToFactor | Source code |
| .countIn | Source code |
| .destandardise | Source code |
| .entropy | Source code |
| .estSigma | Source code |
| .expDist | Source code |
| .expand | Source code |
| .expand2 | Source code |
| .expandCoeff | Source code |
| .expandDat | Source code |
| .expandGenoToDist | Source code |
| .expandGenoToDistAll | Source code |
| .extractIds | Source code |
| .extractIdsMat | Source code |
| .extractIdsVec | Source code |
| .extractNames | Source code |
| .extractSig | Source code |
| .extractSig1 | Source code |
| .extractSig1P | Source code |
| .extractSigExact | Source code |
| .extractSigP | Source code |
| .fillMissing | Source code |
| .findIn | Source code |
| .findInclusion | Source code |
| .findInd | Source code |
| .findmax | Source code |
| .fisherPvalue | Source code |
| .fixDuplicatesInTodo | Source code |
| .fixGenoCols | Source code |
| .fixNonNumeric | Source code |
| .flatten | Source code |
| .flattenBetaX | Source code |
| .formatTable | Source code |
| .fprint | Source code |
| .genRandCovar | Source code |
| .getArray | Source code |
| .getAvg | Source code |
| .getAvgAll | Source code |
| .getAvgWeights | Source code |
| .getCNProfile | Source code |
| .getDim | Source code |
| .getFamily | Source code |
| .getGlm | Source code |
| .getHWE | Source code |
| .getHist | Source code |
| .getIMatrix | Source code |
| .getIncl | Source code |
| .getLast | Source code |
| .getLimitMatrixFromList | Source code |
| .getMaf | Source code |
| .getOnes | Source code |
| .getPv | Source code |
| .getPvLrr | Source code |
| .getPvLrrAllGen | Source code |
| .getPvLrrMult | Source code |
| .getPvLrrMultiGen | Source code |
| .getPvLrrMultiGen1 | Source code |
| .getPvLrrMultiGenNoVS | Source code |
| .getPvLrrMultiGenVS | Source code |
| .getPvRev | Source code |
| .getPvRevPleio | Source code |
| .getPvRevPleioVS | Source code |
| .getPvRevPleio_ | Source code |
| .getPvTable | Source code |
| .getSuffix | Source code |
| .getSumBetaX | Source code |
| .getUNum1Matrix | Source code |
| .getVCFDimNames | Source code |
| .getVCFProcess | Source code |
| .getVCFSplit | Source code |
| .getin | Source code |
| .getin1 | Source code |
| .getin2 | Source code |
| .glm1 | Source code |
| .gs | Source code |
| .heatm | Source code |
| .hwep | Source code |
| .hwepall | Source code |
| .hwestat | Source code |
| .iscase | Source code |
| .joinRes | Source code |
| .joinResVec | Source code |
| .length | Source code |
| .lrt | Source code |
| .mPhen | Source code |
| .mabf | Source code |
| .mafCount | Source code |
| .makeColsForBed | Source code |
| .makeFactor | Source code |
| .makeGenoWeights | Source code |
| .makeNumeric | Source code |
| .makeQuantile | Source code |
| .makeThresh | Source code |
| .makeTopTail | Source code |
| .manh | Source code |
| .manhattan | Source code |
| .manhattanBed | Source code |
| .mergeAlleleCols | Source code |
| .mergeFiles | Source code |
| .mergeLists | Source code |
| .metaAnalysis | Source code |
| .metaresFisher | Source code |
| .metaresHetMeasure | Source code |
| .metaresInvVarianceFixed | Source code |
| .minOneMinus | Source code |
| .mod | Source code |
| .mod1 | Source code |
| .nonNumeric | Source code |
| .nonNumeric1 | Source code |
| .nullDim | Source code |
| .numLev | Source code |
| .nyholdtSidak | Source code |
| .openGenoConnection | Source code |
| .openOutputConnection | Source code |
| .openPlinkConnection | Source code |
| .openVCFConnection | Source code |
| .openZipConnection | Source code |
| .ordTest | Source code |
| .ordTest1 | Source code |
| .ordTest2 | Source code |
| .ordTestUnivariate | Source code |
| .orthogonalise | Source code |
| .pFromSEBeta | Source code |
| .parseOpts | Source code |
| .plotBaf | Source code |
| .plotFingerprint | Source code |
| .pow | Source code |
| .proc | Source code |
| .proc1 | Source code |
| .projOut | Source code |
| .pseudoInv | Source code |
| .qb | Source code |
| Source code | |
| .qqplot | Source code |
| .readGenoConnection | Source code |
| .readHeader | Source code |
| .readLimitFile | Source code |
| .readLinesPlink | Source code |
| .readPhen | Source code |
| .readPlinkConnection | Source code |
| .readVCFConnection | Source code |
| .readZip | Source code |
| .readZipConnection | Source code |
| .reduceWeightsToGeno | Source code |
| .reopenConnection | Source code |
| .rescale | Source code |
| .sampDirichlet | Source code |
| .sampJoint | Source code |
| .sample1 | Source code |
| .seFromPBeta | Source code |
| .splitImputed | Source code |
| .standardise | Source code |
| .subSample | Source code |
| .sum1 | Source code |
| .summariseBootstrap | Source code |
| .tabulateWithWeights | Source code |
| .trL | Source code |
| .unchanged | Source code |
| .updateRelatedness | Source code |
| .updateSampleQC | Source code |
| .writeBed | Source code |
| .writeTable | Source code |
| MultiPhen | Man page |
| MultiPhen-internal | Man page |
| MultiPhen-package | Man page |
| mPhen | Man page Source code |
| mPhen.assoc | Man page Man page Source code |
| mPhen.cca | Man page Source code |
| mPhen.defineOptions | Man page Source code |
| mPhen.options | Man page Source code |
| mPhen.plotCorrelation | Man page Source code |
| mPhen.preparePheno | Man page Source code |
| mPhen.readGenotypes | Man page Source code |
| mPhen.readPhenoFiles | Man page Source code |
| mPhen.sampleCovar | Man page Source code |
| mPhen.sampleGeno | Man page Source code |
| mPhen.simulate | Man page Source code |
| mPhen.writeOutput | Man page Source code |
| pheno | Man page |
| read.plink | Man page Source code |
| snps | Man page |
| snps.imputed | Man page |
