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 |
| 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-devel (arm64): iCARH_2.0.2.1.tgz, r-release (arm64): iCARH_2.0.2.1.tgz, r-oldrel (arm64): iCARH_2.0.2.1.tgz, r-devel (x86_64): 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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