strum: STRUctural Modeling of Latent Variables for General Pedigree

Implements a broad class of latent variable and structural equation models for general pedigree data.

AuthorNathan Morris [aut, cre], Yeunjoo Song [aut], Stephen Cahn [ctb]
Date of publication2015-06-12 06:43:35
MaintainerNathan Morris <nathan.morris@cwru.edu>
LicenseGPL (>= 2)
Version0.6.2

View on CRAN

Functions

allRandomEffects Man page
allRandomEffects<- Man page
allRandomEffects<-,strumVirtualModel-method Man page
allRandomEffects,strumVirtualModel-method Man page
ascertainment Man page
ascertainment<- Man page
ascertainment<-,strumVirtualModel-method Man page
ascertainment,strumVirtualModel-method Man page
coding Man page
coding<- Man page
coding<-,strumMarker-method Man page
coding,strumMarker-method Man page
covariatePhenotypes Man page
covariatePhenotypes,strumVirtualModel-method Man page
createSimModel Man page
createStrumData Man page
createStrumMarker Man page
createStrumModel Man page
dataType Man page
dataType<- Man page
dataType<-,strumData-method Man page
dataType,strumData-method Man page
dataVals Man page
dataVals<- Man page
dataVals<-,strumData-method Man page
dataVals,strumData-method Man page
errorRate Man page
errorRate<- Man page
errorRate<-,strumMarker-method Man page
errorRate,strumMarker-method Man page
fittedParameters Man page
fittedParameters<- Man page
fittedParametersCovMatrix Man page
fittedParametersCovMatrix<- Man page
fittedParametersCovMatrix<-,strumFittedModel-method Man page
fittedParametersCovMatrix,strumFittedModel-method Man page
fittedParameters<-,strumFittedModel-method Man page
fittedParameters,strumFittedModel-method Man page
formulas Man page
formulas<- Man page
formulas<-,strumVirtualModel-method Man page
formulas,strumVirtualModel-method Man page
haplotypes Man page
haplotypes<- Man page
haplotypes<-,strumMarker-method Man page
haplotypes,strumMarker-method Man page
ibd Man page
ibdMarker Man page
ibdMarker<- Man page
ibdMarker<-,strumIBD-method Man page
ibdMarker,strumIBD-method Man page
ibdMatrix Man page
ibdMatrix<- Man page
ibdMatrix<-,strumIBD-method Man page
ibdMatrix,strumIBD-method Man page
ibd,strumData-method Man page
importHapmapData Man page
importIBD Man page
importIBD,strumData-method Man page
intervalIBD Man page
intervalIBD<- Man page
intervalIBD<-,strumMarker-method Man page
intervalIBD,strumMarker-method Man page
markerFacts Man page
markerFacts<- Man page
markerFacts<-,strumMarker-method Man page
markerFacts,strumMarker-method Man page
markerInfo Man page
markerInfo<- Man page
markerInfo<-,strumSimModel-method Man page
markerInfo,strumSimModel-method Man page
missingRate Man page
missingRate<- Man page
missingRate<-,strumMarker-method Man page
missingRate,strumMarker-method Man page
mutationRate Man page
mutationRate<- Man page
mutationRate<-,strumMarker-method Man page
mutationRate,strumMarker-method Man page
paramNames Man page
paramNames<- Man page
paramNames<-,strumVirtualModel-method Man page
paramNames,strumVirtualModel-method Man page
phi Man page
phi<- Man page
phi<-,strumData-method Man page
phi,strumData-method Man page
plot,strumModel-method Man page
plot,strumSimModel-method Man page
plot,strumVirtualModel-method Man page
populationRecombRate Man page
populationRecombRate<- Man page
populationRecombRate<-,strumMarker-method Man page
populationRecombRate,strumMarker-method Man page
returnIBD Man page
returnIBD<- Man page
returnIBD<-,strumMarker-method 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
simulateStrumData Man page
strum Man page
[<-,strumData,ANY,ANY,ANY-method Man page
[,strumData,ANY,ANY,ANY-method Man page
strumData-class Man page
[[<-,strumData-method Man page
[[,strumData-method Man page
$<-,strumData-method Man page
$,strumData-method Man page
strumFittedModel-class Man page
strumIBD-class Man page
strumMarker-class Man page
strumModel-class Man page
strum-package Man page
strumSimModel-class Man page
strumVirtualModel-class Man page
traitMissingRate Man page
traitMissingRate<- Man page
traitMissingRate<-,strumSimModel-method Man page
traitMissingRate,strumSimModel-method Man page
varList Man page
varList<- Man page
varList<-,strumVirtualModel-method Man page
varList,strumVirtualModel-method Man page

Files

strum
strum/inst
strum/inst/extdata
strum/inst/extdata/hap20snp10.Rdata
strum/inst/extdata/example_ped.csv
strum/inst/extdata/example_raw.csv
strum/inst/extdata/GENIBD.chr1Ped.ibd
strum/inst/doc
strum/inst/doc/strum-example.R
strum/inst/doc/strum-intro.R
strum/inst/doc/strum-intro.Rnw
strum/inst/doc/strum-example.Rnw
strum/inst/doc/strum-example.pdf
strum/inst/doc/strum-intro.pdf
strum/inst/include
strum/inst/include/utils.h
strum/src
strum/src/Makevars
strum/src/computeInterval.cpp
strum/src/computeLLDeriv.cpp
strum/src/computeQ.cpp
strum/src/Makevars.win
strum/NAMESPACE
strum/R
strum/R/strum.R strum/R/06strumData.R strum/R/utils.R strum/R/estimateCovariance.R strum/R/02strumModel.R strum/R/03strumFittedModel.R strum/R/estimateDerivative.R strum/R/01strumSimModel.R strum/R/fitModel.R strum/R/estimateParameter.R strum/R/05strumIBD.R strum/R/createModel.R strum/R/simulateData.R strum/R/00strumVirtualModel.R strum/R/generateStartValue.R strum/R/04strumMarker.R strum/R/createMarker.R strum/R/createData.R
strum/vignettes
strum/vignettes/figures
strum/vignettes/figures/fig_linkage.png
strum/vignettes/figures/fig_model7.png
strum/vignettes/figures/fig_association.png
strum/vignettes/figures/fig_model4.png
strum/vignettes/figures/fig_model8.png
strum/vignettes/figures/fig_model1.png
strum/vignettes/figures/fig_model9.png
strum/vignettes/figures/fig_model0.png
strum/vignettes/figures/fig_model3.png
strum/vignettes/figures/fig_model5.png
strum/vignettes/figures/fig_model6.png
strum/vignettes/figures/fig_model2.png
strum/vignettes/strum-intro.Rnw
strum/vignettes/strum-example.Rnw
strum/MD5
strum/build
strum/build/vignette.rds
strum/DESCRIPTION
strum/ChangeLog
strum/man
strum/man/strumVirtualModel-class.Rd strum/man/simulateStrumData.Rd strum/man/strumMarker-class.Rd strum/man/createStrumData.Rd strum/man/strum.Rd strum/man/strumData-class.Rd strum/man/importHapmapData.Rd strum/man/strumModel-class.Rd strum/man/createSimModel.Rd strum/man/createStrumModel.Rd strum/man/strum-package.Rd strum/man/createStrumMarker.Rd strum/man/strumFittedModel-class.Rd strum/man/strumSimModel-class.Rd strum/man/strumIBD-class.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.