Package: MultiPhen 2.0.3

Lachlan Coin

MultiPhen: A Package to Test for Multi-Trait Association

Performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model).

Authors:Lachlan Coin, Paul O'Reilly, Yotsawat Pompyen, Clive Hoggart and Federico Calboli

MultiPhen_2.0.3.tar.gz
MultiPhen_2.0.3.tar.gz(r-4.5-noble)MultiPhen_2.0.3.tar.gz(r-4.4-noble)
MultiPhen_2.0.3.tgz(r-4.4-emscripten)MultiPhen_2.0.3.tgz(r-4.3-emscripten)
MultiPhen.pdf |MultiPhen.html
MultiPhen/json (API)

# Install 'MultiPhen' in R:
install.packages('MultiPhen', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • pheno - A dummy phenotype dataset that provides an example of the input phenotype data used by the package
  • snps - A dummy snp dataset that provides an example of the input snp data used by the package
  • snps.imputed - Imputed SNP dataset

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.93 score 17 scripts 261 downloads 29 mentions 199 exports 73 dependencies

Last updated 5 years agofrom:c365747889. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-linuxNOTENov 04 2024

Exports:.abf.abfSig.allFreq.applySidakCorrection.applyTrans.as.numeric1.backwardSelection.bafratio.calcExpectedGeno.calcOffset.calcPPA.centralise.chol.cholesky.closeGenoConnection.cnt.cntNa.cntVec.cnvdistr.convAvgToUnc.convAvgToUncM.convAvgToUncMat.convertFactorToMatrix.convertMatrixToFactor.countIn.destandardise.entropy.estSigma.expand.expand2.expandCoeff.expandDat.expandGenoToDist.expandGenoToDistAll.expDist.extractIds.extractIdsMat.extractIdsVec.extractNames.extractSig.extractSig1.extractSig1P.extractSigExact.extractSigP.fillMissing.findIn.findInclusion.findInd.findmax.fisherPvalue.fixDuplicatesInTodo.fixGenoCols.fixNonNumeric.flatten.flattenBetaX.formatTable.fprint.genRandCovar.getArray.getAvg.getAvgAll.getAvgWeights.getCNProfile.getDim.getFamily.getGlm.getHist.getHWE.getIMatrix.getin.getin1.getin2.getIncl.getLast.getLimitMatrixFromList.getMaf.getOnes.getPv.getPvLrr.getPvLrrAllGen.getPvLrrMult.getPvLrrMultiGen.getPvLrrMultiGen1.getPvLrrMultiGenNoVS.getPvLrrMultiGenVS.getPvRev.getPvRevPleio.getPvRevPleio_.getPvRevPleioVS.getPvTable.getSuffix.getSumBetaX.getUNum1Matrix.getVCFDimNames.getVCFProcess.getVCFSplit.glm1.gs.heatm.hwep.hwepall.hwestat.iscase.joinRes.joinResVec.length.lrt.mabf.mafCount.makeColsForBed.makeFactor.makeGenoWeights.makeNumeric.makeQuantile.makeThresh.makeTopTail.manh.manhattan.manhattanBed.mergeAlleleCols.mergeFiles.mergeLists.metaAnalysis.metaresFisher.metaresHetMeasure.metaresInvVarianceFixed.minOneMinus.mod.mod1.mPhen.nonNumeric.nonNumeric1.nullDim.numLev.nyholdtSidak.openGenoConnection.openOutputConnection.openPlinkConnection.openVCFConnection.openZipConnection.ordTest.ordTest1.ordTest2.ordTestUnivariate.orthogonalise.parseOpts.pFromSEBeta.plotBaf.plotFingerprint.pow.proc.proc1.projOut.pseudoInv.qb.qq.qqplot.readGenoConnection.readHeader.readLimitFile.readLinesPlink.readPhen.readPlinkConnection.readVCFConnection.readZip.readZipConnection.reduceWeightsToGeno.reopenConnection.rescale.sampDirichlet.sampJoint.sample1.seFromPBeta.splitImputed.standardise.subSample.sum1.summariseBootstrap.tabulateWithWeights.trL.unchanged.updateRelatedness.updateSampleQC.writeBed.writeTablemPhenmPhen.assocmPhen.ccamPhen.defineOptionsmPhen.optionsmPhen.plotCorrelationmPhen.preparePhenomPhen.readGenotypesmPhen.readPhenoFilesmPhen.sampleCovarmPhen.sampleGenomPhen.simulatemPhen.writeOutputread.plink

Dependencies:abindbackportsbitbit64bootbroomclicliprcodetoolsCompQuadFormcpp11crayondplyrepitoolsfansiforcatsforeachgenericsglmnetglueHardyWeinberghavenhmsiteratorsjomolatticelifecyclelme4magrittrMASSmathjaxrMatrixmetametadatmetaformiceminqamitmlnlmenloptrnnetnumDerivordinalpanpbapplypillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRcppEigenreadrrlangrpartRsolnpshapestringistringrsurvivaltibbletidyrtidyselecttruncnormtzdbucminfutf8vctrsvroomwithrxml2

Using MultiPhen for simulation

Rendered fromMultiPhen.Rnwusingutils::Sweaveon Nov 04 2024.

Last update: 2014-01-08
Started: 2014-01-08