Package: PrInCE 1.29.0

Michael Skinnider

PrInCE: Predicting Interactomes from Co-Elution

PrInCE (Predicting Interactomes from Co-Elution) uses a naive Bayes classifier trained on dataset-derived features to recover protein-protein interactions from co-elution chromatogram profiles. This package contains the R implementation of PrInCE.

Authors:Michael Skinnider [aut, trl, cre], R. Greg Stacey [ctb], Nichollas Scott [ctb], Anders Kristensen [ctb], Leonard Foster [aut, led]

PrInCE_1.29.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
PrInCE/json (API)

# Install 'PrInCE' in R:

install.packages('PrInCE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fosterlab/prince/issues

Datasets:

gold_standard - Reference set of human protein complexes
kristensen - Interactome of HeLa cells
kristensen_gaussians - Fitted Gaussian mixture models for the 'kristensen' dataset
scott - Cytoplasmic interactome of Jurkat T cells during apoptosis
scott_gaussians - Fitted Gaussian mixture models for the 'scott' dataset

On BioConductor:PrInCE-1.29.0(bioc 3.24)PrInCE-1.28.0(bioc 3.23)

proteomics systemsbiology networkinference

6.78 score 8 stars 63 scripts 367 downloads 6 mentions 29 exports 161 dependencies

Last updated from:9fd4073a2e. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	209
linux-devel-x86_64	WARNING	634
source / vignettes	OK	393
linux-release-x86_64	WARNING	446
macos-release-arm64	WARNING	312
macos-oldrel-arm64	WARNING	281
windows-devel	WARNING	372
windows-release	WARNING	342
windows-oldrel	WARNING	348
wasm-release	OK	169

Exports:adjacency_matrix_from_data_frame adjacency_matrix_from_list build_gaussians calculate_autocorrelation calculate_features calculate_precision check_gaussians choose_gaussians clean_profile clean_profiles co_apex concatenate_features detect_complexes filter_profiles fit_curve fit_gaussians impute_neighbors is_unweighted is_weighted make_feature_from_data_frame make_feature_from_expression make_initial_conditions make_labels match_matrix_dimensions predict_ensemble predict_interactions PrInCE replace_missing_data threshold_precision

Dependencies:abind affy affyio AnnotationFilter askpass backports base64enc BH biglm Biobase BiocBaseUtils BiocGenerics biocmake BiocManager BiocParallel bslib cachem checkmate cli clue cluster codetools colorspace cpp11 crayon crosstalk curl data.table DBI DelayedArray DEoptimR digest dir.expiry doParallel dplyr evaluate farver fastmap filelock fontawesome foreach forecast foreign formatR Formula fracdiff fs futile.logger futile.options generics GenomicRanges ggplot2 glue gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr igraph impute IRanges isoband iterators jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval LiblineaR lifecycle limma lmtest magrittr MALDIquant MASS Matrix MatrixGenerics matrixStats memoise MetaboCoreUtils mime MsCoreUtils MSnbase MultiAssayExperiment mzID mzR naivebayes ncdf4 nlme nnet openssl otel pcaMethods pillar pkgconfig plotly plyr preprocessCore prettyunits progress promises ProtGenerics PSMatch PTMods purrr QFeatures R6 ranger rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reshape2 Rhdf5lib rlang rmarkdown robustbase rpart rstudioapi S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray Spectra speedglm statmod stringi stringr SummarizedExperiment sys tester tibble tidyr tidyselect timeDate tinytex urca utf8 vctrs viridisLite vsn withr xfun XML XVector yaml zoo

Interactome reconstruction from co-elution data with PrInCE

Rendered fromintro-to-prince.Rmdusingknitr::rmarkdown

Last update: 2019-03-12
Started: 2018-12-18

Citation

Development and contributors

Readme and manuals

Help Manual

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