STRUctural Modeling of Latent Variables for General Pedigree


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Documentation for package ‘strum’ version 0.6.2

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A C D E F H I M P R S T V misc

strum-package A Package for STRUctural Modeling of Latent Variables for General Pedigree Data

-- A --

allRandomEffects Class '"strumVirtualModel"'
allRandomEffects-method Class '"strumVirtualModel"'
allRandomEffects<- Class '"strumVirtualModel"'
allRandomEffects<--method Class '"strumVirtualModel"'
ascertainment Class '"strumVirtualModel"'
ascertainment-method Class '"strumVirtualModel"'
ascertainment<- Class '"strumVirtualModel"'
ascertainment<--method Class '"strumVirtualModel"'

-- C --

coding Class '"strumMarker"'
coding-method Class '"strumMarker"'
coding<- Class '"strumMarker"'
coding<--method Class '"strumMarker"'
covariatePhenotypes Class '"strumVirtualModel"'
covariatePhenotypes-method Class '"strumVirtualModel"'
createSimModel Create strumSimModel Object
createStrumData Create strumData Object
createStrumMarker Create strumMarker Object
createStrumModel Create strumModel Object

-- D --

dataType Class '"strumData"'
dataType-method Class '"strumData"'
dataType<- Class '"strumData"'
dataType<--method Class '"strumData"'
dataVals Class '"strumData"'
dataVals-method Class '"strumData"'
dataVals<- Class '"strumData"'
dataVals<--method Class '"strumData"'

-- E --

errorRate Class '"strumMarker"'
errorRate-method Class '"strumMarker"'
errorRate<- Class '"strumMarker"'
errorRate<--method Class '"strumMarker"'

-- F --

fittedParameters Class '"strumFittedModel"'
fittedParameters-method Class '"strumFittedModel"'
fittedParameters<- Class '"strumFittedModel"'
fittedParameters<--method Class '"strumFittedModel"'
fittedParametersCovMatrix Class '"strumFittedModel"'
fittedParametersCovMatrix-method Class '"strumFittedModel"'
fittedParametersCovMatrix<- Class '"strumFittedModel"'
fittedParametersCovMatrix<--method Class '"strumFittedModel"'
formulas Class '"strumVirtualModel"'
formulas-method Class '"strumVirtualModel"'
formulas<- Class '"strumVirtualModel"'
formulas<--method Class '"strumVirtualModel"'

-- H --

haplotypes Class '"strumMarker"'
haplotypes-method Class '"strumMarker"'
haplotypes<- Class '"strumMarker"'
haplotypes<--method Class '"strumMarker"'

-- I --

ibd Class '"strumData"'
ibd-method Class '"strumData"'
ibdMarker Class '"strumIBD"'
ibdMarker-method Class '"strumIBD"'
ibdMarker<- Class '"strumIBD"'
ibdMarker<--method Class '"strumIBD"'
ibdMatrix Class '"strumIBD"'
ibdMatrix-method Class '"strumIBD"'
ibdMatrix<- Class '"strumIBD"'
ibdMatrix<--method Class '"strumIBD"'
importHapmapData Import Hapmap Data
importIBD Class '"strumData"'
importIBD-method Class '"strumData"'
intervalIBD Class '"strumMarker"'
intervalIBD-method Class '"strumMarker"'
intervalIBD<- Class '"strumMarker"'
intervalIBD<--method Class '"strumMarker"'

-- M --

markerFacts Class '"strumMarker"'
markerFacts-method Class '"strumMarker"'
markerFacts<- Class '"strumMarker"'
markerFacts<--method Class '"strumMarker"'
markerInfo Class '"strumSimModel"'
markerInfo-method Class '"strumSimModel"'
markerInfo<- Class '"strumSimModel"'
markerInfo<--method Class '"strumSimModel"'
missingRate Class '"strumMarker"'
missingRate-method Class '"strumMarker"'
missingRate<- Class '"strumMarker"'
missingRate<--method Class '"strumMarker"'
mutationRate Class '"strumMarker"'
mutationRate-method Class '"strumMarker"'
mutationRate<- Class '"strumMarker"'
mutationRate<--method Class '"strumMarker"'

-- P --

paramNames Class '"strumVirtualModel"'
paramNames-method Class '"strumVirtualModel"'
paramNames<- Class '"strumVirtualModel"'
paramNames<--method Class '"strumVirtualModel"'
phi Class '"strumData"'
phi-method Class '"strumData"'
phi<- Class '"strumData"'
phi<--method Class '"strumData"'
plot-method Class '"strumModel"'
plot-method Class '"strumSimModel"'
plot-method Class '"strumVirtualModel"'
populationRecombRate Class '"strumMarker"'
populationRecombRate-method Class '"strumMarker"'
populationRecombRate<- Class '"strumMarker"'
populationRecombRate<--method Class '"strumMarker"'

-- R --

returnIBD Class '"strumMarker"'
returnIBD-method Class '"strumMarker"'
returnIBD<- Class '"strumMarker"'
returnIBD<--method Class '"strumMarker"'

-- S --

show-method Class '"strumData"'
show-method Class '"strumFittedModel"'
show-method Class '"strumIBD"'
show-method Class '"strumMarker"'
show-method Class '"strumModel"'
show-method Class '"strumSimModel"'
show-method Class '"strumVirtualModel"'
simulateStrumData Simulate strumData Object
strum STRUctural Modeling of Latent Variables for Family Data
strumData-class Class '"strumData"'
strumFittedModel-class Class '"strumFittedModel"'
strumIBD-class Class '"strumIBD"'
strumMarker-class Class '"strumMarker"'
strumModel-class Class '"strumModel"'
strumSimModel-class Class '"strumSimModel"'
strumVirtualModel-class Class '"strumVirtualModel"'

-- T --

traitMissingRate Class '"strumSimModel"'
traitMissingRate-method Class '"strumSimModel"'
traitMissingRate<- Class '"strumSimModel"'
traitMissingRate<--method Class '"strumSimModel"'

-- V --

varList Class '"strumVirtualModel"'
varList-method Class '"strumVirtualModel"'
varList<- Class '"strumVirtualModel"'
varList<--method Class '"strumVirtualModel"'

-- misc --

$-method Class '"strumData"'
$<--method Class '"strumData"'
[-method Class '"strumData"'
[<--method Class '"strumData"'
[[-method Class '"strumData"'
[[<--method Class '"strumData"'