Man pages for const-ae/proDD
Identifying Differentially Abundant Proteins from Label-Free Mass Spectrometry Data
| as_replicate | Get numeric vector with the count of the replicate for each... |
| calc_df_eff | Calculate the effective degrees of freedom |
| calculate_posterior | Internal function that does the actual work for... |
| distance_sq | Square distance between two Gaussian distributions |
| dist_approx | Distance matrix computation respecting non-random missing... |
| dprobdropout | Density of the probabilistic dropout distribution |
| find_approx_for_missing | Find a Gaussian approximation for each missing value in X |
| fit_feature_means | Estimate the mean for each feature |
| fit_feature_mean_uncertainties | Calculate the variance of the mean estimator |
| fit_feature_variances | Find the most likely variance explaining the values for each... |
| fit_global_dropout_curves | Find the inverse probit parameters that best explain the... |
| fit_location_prior | Fit a Gaussian location prior over all samples |
| fit_parameters | Fit the probabilistic dropout parameters |
| fit_unregularized_feature_means | Calculate the unregularized means for all rows for which mup... |
| fit_unregularized_feature_variances | Find the variance without using the regularization |
| fit_variance_prior | Fit a inverse Chi-squared variance prior |
| generate_synthetic_data | Generate a data set according to the probabilistic dropout... |
| invprobit | Inverse probit function |
| match_probdropout_skewed_normal | Match a skewed normal distribution to the probabilistic... |
| mean_probdropout | Find the mean of of the probabilistic dropout distribution... |
| median_normalization | Column wise median normalization of the data matrix |
| mode_probdropout | Find the mode of the probabilistic dropout distribution... |
| mply_dbl | apply function that always returns a numeric matrix |
| predict_feature_parameters | Find feature parameters for elements of X with a fixed set of... |
| print.prodd_parameters | Collection of parameters generated when fitting the... |
| resampling_test | Test the difference between x and y using resampling. |
| sample_protein_means | Estimate the mean of each protein and condtion using MCMC... |
| test_diff | Test difference between two posterior distribution |
| transform_parameters | Update the experimental_design of a parameter object |
| variance_probdropout | Find the variance of of the probabilistic dropout... |
