Bayesian Hierarchical Modeling for Label-Free Proteomics


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Documentation for package ‘baldur’ version 0.0.1

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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