Package: iCARH 2.0.2.1

iCARH: Integrative Conditional Autoregressive Horseshoe Model

Implements the integrative conditional autoregressive horseshoe model discussed in Jendoubi, T., Ebbels, T.M. Integrative analysis of time course metabolic data and biomarker discovery. BMC Bioinformatics 21, 11 (2020) <doi:10.1186/s12859-019-3333-0>. The model consists in three levels: Metabolic pathways level modeling interdependencies between variables via a conditional auto-regressive (CAR) component, integrative analysis level to identify potential associations between heterogeneous omic variables via a Horseshoe prior and experimental design level to capture experimental design conditions through a mixed-effects model. The package also provides functions to simulate data from the model, construct pathway matrices, post process and plot model parameters.

Authors:Takoua Jendoubi [aut, cre], Timothy M.D. Ebbels [aut]

iCARH_2.0.2.1.tar.gz
iCARH_2.0.2.1.zip(r-4.5)iCARH_2.0.2.1.zip(r-4.4)iCARH_2.0.2.1.zip(r-4.3)
iCARH_2.0.2.1.tgz(r-4.4-any)iCARH_2.0.2.1.tgz(r-4.3-any)
iCARH_2.0.2.1.tar.gz(r-4.5-noble)iCARH_2.0.2.1.tar.gz(r-4.4-noble)
iCARH_2.0.2.1.tgz(r-4.4-emscripten)iCARH_2.0.2.1.tgz(r-4.3-emscripten)
iCARH.pdf |iCARH.html✨
iCARH/json (API)

# Install 'iCARH' in R:
install.packages('iCARH', repos = c('https://takouajendoubi.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 6 scripts 162 downloads 1 mentions 18 exports 97 dependencies

Last updated 4 years agofrom:75dbc3f6d4. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-winOKNov 04 2024
R-4.5-linuxOKNov 04 2024
R-4.4-winOKNov 04 2024
R-4.4-macOKNov 04 2024
R-4.3-winOKNov 04 2024
R-4.3-macOKNov 04 2024

Exports:iCARH.checkNormalityiCARH.checkRhatsiCARH.getARCoeffiCARH.getBetaiCARH.getDataImputationiCARH.getPathwaysCoeffiCARH.getPathwaysMatiCARH.getTreatmentEffectiCARH.madiCARH.modeliCARH.paramsiCARH.plotARCoeffiCARH.plotBetaiCARH.plotDataImputationiCARH.plotPathwayPerturbationiCARH.plotTreatmentEffectiCARH.simulateiCARH.waic

Dependencies:abindbackportsBHBiocGenericsbitopsbootbroomcallrcarcarDatacheckmateclicolorspacecorrplotcowplotcpp11DerivdescdistributionaldoBydplyrfansifarverFormulagenericsggplot2ggpubrggrepelggsciggsignifgluegraphgridExtragtableigraphinlineisobandKEGGgraphlabelinglatticelifecyclelme4loomagrittrMASSMatrixMatrixModelsmatrixStatsmc2dmgcvmicrobenchmarkminqamodelrmunsellmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgbuildpkgconfigplyrpolynomposteriorprocessxpspurrrquantregQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelRCurlreshape2RgraphvizrlangrstanrstatixscalesSparseMStanHeadersstringistringrsurvivaltensorAtibbletidyrtidyselectutf8vctrsviridisLitewithrXML

Example for simulating and running the iCARH model

Rendered fromexample.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2020-08-27
Started: 2019-06-04

Readme and manuals

Help Manual

Help pageTopics
Return model parametersiCARH.getARCoeff iCARH.getBeta iCARH.getDataImputation iCARH.getPathwaysCoeff iCARH.getTreatmentEffect
Builds pathways adjacency matricesiCARH.getPathwaysMat
Runs the integrative CAR Horseshoe modeliCARH.model
Summarize and return model parametersiCARH.params
Postprocess and plot model parametersiCARH.checkNormality iCARH.checkRhats iCARH.mad iCARH.plotARCoeff iCARH.plotBeta iCARH.plotDataImputation iCARH.plotPathwayPerturbation iCARH.plotTreatmentEffect iCARH.waic
Simulates longitudinal data based on the iCARH model.iCARH.simulate