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.

Version: 2.0.2.1
Depends: rstan, MASS, stats, ggplot2, glue
Imports: RCurl, KEGGgraph, igraph, reshape2, mc2d, abind, Matrix
Suggests: knitr, rmarkdown
Published: 2020-08-27
Author: Takoua Jendoubi [aut, cre], Timothy M.D. Ebbels [aut]
Maintainer: Takoua Jendoubi <t.jendoubi14 at imperial.ac.uk>
License: GPL (≥ 3)
NeedsCompilation: no
CRAN checks: iCARH results

Downloads:

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: not available, r-oldrel: iCARH_2.0.2.1.tgz
Old sources: iCARH archive

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