Bayesian Hierarchical Modeling for Label-Free Proteomics

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Documentation for package ‘baldur’ version 0.0.3

• 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