A joint mixture model has been developed by Majumdar et al. (2025) <doi:10.48550/arXiv.2412.17511> that integrates information from gene expression data and methylation data at the modelling stage to capture their inherent dependency structure, enabling simultaneous identification of differentially methylated cytosine-guanine dinucleotide (CpG) sites and differentially expressed genes. The model leverages a joint likelihood function that accounts for the nested structure in the data, with parameter estimation performed using an expectation-maximisation algorithm.
| Version: | 1.0.0 |
| Depends: | R (≥ 3.5.0) |
| Imports: | foreach, doParallel, parallel, mclust, stats, utils, edgeR, magrittr, ggplot2, scales, tidyr, dplyr, reshape2, gridExtra, grid, tidyselect, cowplot |
| Suggests: | rmarkdown, knitr |
| Published: | 2025-01-13 |
| DOI: | 10.32614/CRAN.package.idiffomix |
| Author: | Koyel Majumdar [cre, aut], Isobel Claire Gorley [aut], Thomas Brendan Murphy [aut], Florence Jaffrezic [aut], Andrea Rau [aut] |
| Maintainer: | Koyel Majumdar <koyelmajumdar.phdresearch at gmail.com> |
| License: | GPL-3 |
| NeedsCompilation: | yes |
| CRAN checks: | idiffomix results |
| Reference manual: | idiffomix.pdf |
| Vignettes: |
idiffomix: integrated differential analysis of multi-omics data using a joint mixture model (source, R code) |
| Package source: | idiffomix_1.0.0.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): idiffomix_1.0.0.tgz, r-oldrel (x86_64): idiffomix_1.0.0.tgz |
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