Man pages for fosterlab/PrInCE-R
Predicting Interactomes from Co-Elution
| adjacency_matrix_from_data_frame | Create an adjacency matrix from a data frame |
| adjacency_matrix_from_list | Create an adjacency matrix from a list of complexes |
| aic | Model selection for Gaussian mixture models |
| build_gaussians | Deconvolve profiles into Gaussian mixture models |
| calculate_autocorrelation | Calculate the autocorrelation for each protein between a pair... |
| calculate_features | Calculate the default features used to predict interactions... |
| calculate_precision | Calculate precision at each point in a sequence |
| check_gaussians | Check the format of a list of Gaussians |
| choose_gaussians | Fit a Gaussian mixture model to a co-elution profile |
| clean_profile | Preprocess a co-elution profile |
| clean_profiles | Preprocess a co-elution profile matrix |
| co_apex | Calculate the co-apex score for every protein pair |
| concatenate_features | Combine features across multiple replicates |
| detect_complexes | Detect significantly interacting complexes in a chromatogram... |
| filter_profiles | Filter a co-elution profile matrix |
| fit_curve | Output the fit curve for a given mixture of Gaussians |
| fit_gaussians | Fit a mixture of Gaussians to a chromatogram curve |
| gold_standard | Reference set of human protein complexes |
| impute_neighbors | Impute single missing values |
| is_unweighted | Test whether a network is unweighted |
| is_weighted | Test whether a network is weighted |
| kristensen | Interactome of HeLa cells |
| kristensen_gaussians | Fitted Gaussian mixture models for the 'kristensen' dataset |
| make_feature_from_data_frame | Create a feature vector for a classifier from a data frame |
| make_feature_from_expression | Create a feature vector from expression data |
| make_initial_conditions | Make initial conditions for curve fitting with a mixture of... |
| make_labels | Make labels for a classifier based on a gold standard |
| match_matrix_dimensions | Match the dimensions of a query matrix to a profile matrix |
| predict_ensemble | Predict interactions using an ensemble of classifiers |
| predict_interactions | Predict interactions given a set of features and examples |
| PrInCE | PrInCE: Prediction of Interactomes from Co-Elution |
| replace_missing_data | Replace missing data with median ± random noise |
| scott | Cytoplasmic interactome of Jurkat T cells during apoptosis |
| scott_gaussians | Fitted Gaussian mixture models for the 'scott' dataset |
| threshold_precision | Threshold interactions at a given precision cutoff |
