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.

Depends: rstan, MASS, stats, ggplot2, glue
Imports: RCurl, KEGGgraph, igraph, reshape2, mc2d, abind, Matrix
Suggests: knitr, rmarkdown
Published: 2020-08-27
DOI: 10.32614/CRAN.package.iCARH
Author: Takoua Jendoubi [aut, cre], Timothy M.D. Ebbels [aut]
Maintainer: Takoua Jendoubi <t.jendoubi14 at imperial.ac.uk>
License: GPL (≥ 3)
NeedsCompilation: no
In views: Omics
CRAN checks: iCARH results


Reference manual: iCARH.pdf
Vignettes: Example of simulating and running the iCARH model


Package source: iCARH_2.0.2.1.tar.gz
Windows binaries: r-devel: iCARH_2.0.2.1.zip, r-release: iCARH_2.0.2.1.zip, r-oldrel: iCARH_2.0.2.1.zip
macOS binaries: r-release (arm64): iCARH_2.0.2.1.tgz, r-oldrel (arm64): iCARH_2.0.2.1.tgz, r-release (x86_64): iCARH_2.0.2.1.tgz, r-oldrel (x86_64): iCARH_2.0.2.1.tgz
Old sources: iCARH archive


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