API for strum
STRUctural Modeling of Latent Variables for General Pedigree

Global functions
$,strumData-method Man page
$<-,strumData-method Man page
[,strumData,ANY,ANY,ANY-method Man page
[<-,strumData,ANY,ANY,ANY-method Man page
[[,strumData-method Man page
[[<-,strumData-method Man page
addVC Source code
allRandomEffects Man page
allRandomEffects,strumVirtualModel-method Man page
allRandomEffects<- Man page
allRandomEffects<-,strumVirtualModel-method Man page
ascertainment Man page
ascertainment,strumVirtualModel-method Man page
ascertainment<- Man page
ascertainment<-,strumVirtualModel-method Man page
buildThToThB Source code
buildVarList Source code
checkPed Source code
coding Man page
coding,strumMarker-method Man page
coding<- Man page
coding<-,strumMarker-method Man page
computeBivariateLL Source code
computeIntervals Source code
computeUnivariateLL Source code
covariatePhenotypes Man page
covariatePhenotypes,strumVirtualModel-method Man page
createModel Source code
createSimModel Man page Source code
createStrumData Man page Source code
createStrumMarker Man page Source code
createStrumModel Man page Source code
dataType Man page
dataType,strumData-method Man page
dataType<- Man page
dataType<-,strumData-method Man page
dataVals Man page
dataVals,strumData-method Man page
dataVals<- Man page
dataVals<-,strumData-method Man page
doSimpleCheck Source code
errorRate Man page
errorRate,strumMarker-method Man page
errorRate<- Man page
errorRate<-,strumMarker-method Man page
estimateDeltaCovariance Source code
estimateDeltaDerivative Source code
estimateDeltaParameter Source code
estimateThetaCovariance Source code
estimateThetaParameter Source code
filterMissing Source code
filterMissingVC Source code
findDummyMarkerInfo Source code
findMissing Source code
fitModel Source code
fitModelStep1 Source code
fitModelStep2 Source code
fittedParameters Man page
fittedParameters,strumFittedModel-method Man page
fittedParameters<- Man page
fittedParameters<-,strumFittedModel-method Man page
fittedParametersCovMatrix Man page
fittedParametersCovMatrix,strumFittedModel-method Man page
fittedParametersCovMatrix<- Man page
fittedParametersCovMatrix<-,strumFittedModel-method Man page
formulas Man page
formulas,strumVirtualModel-method Man page
formulas<- Man page
formulas<-,strumVirtualModel-method Man page
funDeriv Source code
generateStartValue Source code
getAnalysisVC Source code
getAnalysisX Source code
getAnalysisY Source code
getChiNullCorrect Source code
getCovBlockCount Source code
getFormulaStuff Source code
getIndex Source code
getModelMats Source code
getNodeNames Source code
getParamIndex Source code
getParentPos Source code
getPhi Source code
getRandomError Source code
getTheoCorrectT Source code
getVCFilteredData Source code
getVCNodeEdge Source code
getValidAnalysisData Source code
getYFilteredData Source code
haplotypes Man page
haplotypes,strumMarker-method Man page
haplotypes<- Man page
haplotypes<-,strumMarker-method Man page
ibd Man page
ibd,strumData-method Man page
ibdMarker Man page
ibdMarker,strumIBD-method Man page
ibdMarker<- Man page
ibdMarker<-,strumIBD-method Man page
ibdMatrix Man page
ibdMatrix,strumIBD-method Man page
ibdMatrix<- Man page
ibdMatrix<-,strumIBD-method Man page
importHapmapData Man page Source code
importIBD Man page
importIBD,strumData-method Man page
intervalIBD Man page
intervalIBD,strumMarker-method Man page
intervalIBD<- Man page
intervalIBD<-,strumMarker-method Man page
makeSigmaList Source code
markerFacts Man page
markerFacts,strumMarker-method Man page
markerFacts<- Man page
markerFacts<-,strumMarker-method Man page
markerInfo Man page
markerInfo,strumSimModel-method Man page
markerInfo<- Man page
markerInfo<-,strumSimModel-method Man page
missingRate Man page
missingRate,strumMarker-method Man page
missingRate<- Man page
missingRate<-,strumMarker-method Man page
mportIBDSAGE Source code
mutationRate Man page
mutationRate,strumMarker-method Man page
mutationRate<- Man page
mutationRate<-,strumMarker-method Man page
orderPedigrees Source code
paramNames Man page
paramNames,strumVirtualModel-method Man page
paramNames<- Man page
paramNames<-,strumVirtualModel-method Man page
parseFormulas Source code
phi Man page
phi,strumData-method Man page
phi<- Man page
phi<-,strumData-method Man page
plot,strumModel-method Man page
plot,strumSimModel-method Man page
plot,strumVirtualModel-method Man page
plotModel Source code
populationRecombRate Man page
populationRecombRate,strumMarker-method Man page
populationRecombRate<- Man page
populationRecombRate<-,strumMarker-method Man page
printInfoLine Source code
processEqualConstrSide Source code
rdirichlet Source code
returnIBD Man page
returnIBD,strumMarker-method Man page
returnIBD<- Man page
returnIBD<-,strumMarker-method Man page
show,strumData-method Man page
show,strumFittedModel-method Man page
show,strumIBD-method Man page
show,strumMarker-method Man page
show,strumModel-method Man page
show,strumSimModel-method Man page
show,strumVirtualModel-method Man page
showModel Source code
simulateHaplotypes Source code
simulateMarker Source code
simulateMissing Source code
simulateStrumData Man page Source code
simulateVC Source code
sqrtMat Source code
strum Man page Source code
strum-package Man page
strumData-class Man page
strumFittedModel-class Man page
strumIBD-class Man page
strumMarker-class Man page
strumModel-class Man page
strumNull Source code
strumSimModel-class Man page
strumVirtualModel-class Man page
testModel Source code
testPosDefMatrix Source code
thetaToDelta Source code
traitMissingRate Man page
traitMissingRate,strumSimModel-method Man page
traitMissingRate<- Man page
traitMissingRate<-,strumSimModel-method Man page
trimSpace Source code
varList Man page
varList,strumVirtualModel-method Man page
varList<- Man page
varList<-,strumVirtualModel-method Man page
strum documentation built on May 29, 2017, 8:53 p.m.