Predicting Interactomes from Co-Elution

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Documentation for package ‘PrInCE’ version 1.20.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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 of co-elution experiments.
calculate_features	Calculate the default features used to predict interactions in PrInCE
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
concatenate_features	Combine features across multiple replicates
co_apex	Calculate the co-apex score for every protein pair
detect_complexes	Detect significantly interacting complexes in a chromatogram matrix
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
gaussian_aic	Model selection for Gaussian mixture models
gaussian_aicc	Model selection for Gaussian mixture models
gaussian_bic	Model selection for Gaussian mixture models
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 Gaussians
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