API for MultiPhen
A Package to Test for Pleiotropic Effects

Global functions
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
qq 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
MultiPhen documentation built on May 29, 2017, 10:13 p.m.