baldur: Bayesian Hierarchical Modeling for Label-Free Proteomics
Statistical decision in proteomics data using a hierarchical Bayesian model. There are two regression models for describing the mean-variance trend, a gamma regression or a latent gamma mixture regression. The regression model is then used as an Empirical Bayes estimator for the prior on the variance in a peptide. Further, it assumes that each measurement has an uncertainty (increased variance) associated with it that is also inferred. Finally, it tries to estimate the posterior distribution (by Hamiltonian Monte Carlo) for the differences in means for each peptide in the data. Once the posterior is inferred, it integrates the tails to estimate the probability of error from which a statistical decision can be made. See Berg and Popescu for details (<doi:10.1101/2023.05.11.540411>).
| Version: | 0.0.3 |
| Depends: | R (≥ 4.2.0) |
| Imports: | dplyr (≥ 1.0.9), magrittr (≥ 2.0.3), methods, purrr (≥ 0.3.4), Rcpp (≥ 0.12.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.26.0), rstantools (≥ 2.2.0), stats, stringr (≥ 1.0.4), tidyr (≥ 1.2.0), rlang (≥ 1.0.2), Rdpack (≥ 2.4), multidplyr (≥ 0.1.1), ggplot2 (≥ 3.3.6), tibble (≥ 3.1.7), viridisLite (≥ 0.4.1), lifecycle |
| LinkingTo: | BH (≥ 1.66.0), Rcpp (≥ 0.12.0), RcppEigen (≥ 0.3.3.3.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.26.0), StanHeaders (≥ 2.26.0) |
| Suggests: | knitr, rmarkdown |
| Published: | 2023-09-18 |
| DOI: | 10.32614/CRAN.package.baldur |
| Author: | Philip Berg  [aut,
cre] |
| Maintainer: | Philip Berg <pb1015 at msstate.edu> |
| BugReports: | https://github.com/PhilipBerg/baldur/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/PhilipBerg/baldur |
| NeedsCompilation: | yes |
| SystemRequirements: | GNU make |
| Language: | en-US |
| Materials: | README NEWS |
| CRAN checks: | baldur results |
Documentation:
| Reference manual: | baldur.pdf |
| Vignettes: |
Baldur UPS Tutorial Baldur Yeast Tutorial |
Downloads:
| Package source: | baldur_0.0.3.tar.gz |
| Windows binaries: | r-devel: baldur_0.0.3.zip, r-release: baldur_0.0.3.zip, r-oldrel: baldur_0.0.3.zip |
| macOS binaries: | r-release (arm64): baldur_0.0.3.tgz, r-oldrel (arm64): baldur_0.0.3.tgz, r-release (x86_64): baldur_0.0.3.tgz, r-oldrel (x86_64): baldur_0.0.3.tgz |
| Old sources: | baldur archive |
Linking:
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