A Package to Test for Pleiotropic Effects

Global functions | |
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MultiPhen | Man page |

MultiPhen-internal | Man page |

MultiPhen-package | Man page |

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 |

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 |

joinRes | Source code |

joinResVec | Source code |

lrt | Source code |

mPhen | Man page Source code 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 |

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 |

onAttach | 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 |

pheno | Man page |

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 |

read.plink | Man page 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 |

scase | Source code |

seFromPBeta | Source code |

snps | Man page |

snps.imputed | Man page |

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 |

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