# Bayesian Hierarchical Modeling for Label-Free Proteomics

## Documentation for package ‘baldur’ version 0.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

baldur-package | The 'baldur' package.
baldur | The 'baldur' package.
calculate_mean_sd_trends | Calculate the Mean-Variance trend
coef.lgmr | Fit Latent Gamma Mixture Regression
empirical_bayes | Baldur's empirical Bayes Prior For The Mean In Conditions
estimate_beta | Estimate Gamma hyperparameters for sigma
estimate_beta.glm | Estimate Gamma hyperparameters for sigma
estimate_beta.lgmr | Estimate Gamma hyperparameters for sigma
estimate_gamma_hyperparameters | Estimate Gamma hyperparameters for sigma
estimate_gamma_hyperparameters.glm | Estimate Gamma hyperparameters for sigma
estimate_gamma_hyperparameters.lgmr | Estimate Gamma hyperparameters for sigma
estimate_uncertainty | Estimate measurement uncertainty
estimate_uncertainty.glm | Estimate measurement uncertainty
estimate_uncertainty.lgmr | Estimate measurement uncertainty
fit_gamma_regression | Function for Fitting the Mean-Variance Gamma Regression Models
fit_lgmr | Fit Latent Gamma Mixture Regression
infer_data_and_decision_model | Sample the Posterior of the data and decision model and generate point estimates
lgmr_model | Latent Gamma Regression Model
lgmr_plotting | Visualization of LGMR models
plot_gamma | Function for plotting the gamma regression for the mean-variance trend
plot_gamma_regression | Function for plotting the mean-variance gamma regressions
plot_lgmr_regression | Visualization of LGMR models
plot_regression_field | Visualization of LGMR models
plot_sa | Plot the trend between the log fold-change and sigma, coloring significant hits
plot_volcano | Plot the -log10(err) against the log fold-change
print.lgmr | Fit Latent Gamma Mixture Regression
psrn | Normalize data to a pseudo-reference
ups | Spiked-in data set of peptides
weakly_informative | Baldur's weakly informative prior for the mean in conditions
yeast | Spiked-in data set of reversibly oxidized cysteines