Pathway CollectionsFunctions to create or modify pathway collection objects 


Read a 

Write a 

Manually Create a 

Display the Summary of a 

Subset a 

Creating S4Class Objects and Basic MethodsDescriptions, creators, and accessors of the Omics* S4 classes 

An S4 class for mass spectrometry or bioassay data and gene pathway lists 

An S4 class for survival responses within an 

An S4 class for continuous responses within an 

An S4 class for categorical responses within an 

Check validity of new Omics*class objects 

Transpose an Assay (Data Frame) 

Tidy a SummarizedExperiment Assay 

Generation Wrapper function for 

Display the Summary of an 


Access and Edit Assay or 
Access and Edit Event Time or Indicator in an 

Access and Edit Response of an 

PCAmethod FunctionsFunctions to analyze Omicsclass objects 

Adaptive, elasticnet, sparse principal component analysis 

Test pathway association with AESPCA 

Colon Cancer Omics Data 

Gene Pathway Subset 

Check if a long atomic vector contains a short atomic vector 

Generation Wrapper function for 


Generation functions for 
Manually Create a 

Extract PCs and Loadings from a 

Extract Table of \(p\)values from a 


Access and Edit Assay or 
Access and Edit Response of an 

Access and Edit Event Time or Indicator in an 

Calculate Test Data PCs from TrainingData Estimated Loadings 

An S4 class for categorical responses within an 

An S4 class for mass spectrometry or bioassay data and gene pathway lists 

An S4 class for continuous responses within an 

An S4 class for survival responses within an 

Extract and Test the Significance of PathwaySpecific Principal Components 

Read a 

Tidy a SummarizedExperiment Assay 

Subset a 

Subset PathwaySpecific Data 

Test pathways with Supervised PCA 

Transpose an Assay (Data Frame) 

Filter and Subset a 

Wikipathways Homosapiens EntrezIDs 

Wikipathways Homosapiens Gene Symbols 

Write a 

Example Data SetsData for function examples 

Gene Pathway Subset 

Colon Cancer Omics Data 

Wikipathways Homosapiens EntrezIDs 

Internal AESPCA FunctionsFunctions designed to be called by the AESPCA wrapper above 

Adaptive, elasticnet, sparse principal component analysis 

Least Angle Regression and LASSO Regression 

Extract AESPCs from recorded pathwaysubsets of a mass spectrometry or bioassay data frame 

AESPCA permutation test of survival response for pathway PCs 

AESPCA permutation test of continuous response for pathway PCs 

AESPCA permutation test of categorical response for pathway PCs 

Normalize and reconstruct the eigenvalues of a data matrix for supervised PCA 

Internal Supervised PCA FunctionsFunctions designed to be called by the Supervised PCA wrapper above 

Train Cox Proportional Hazards model for supervised PCA 

Genespecific Regularized Ordinary Least Squares fit statistics for supervised PCA 

Genespecific Generalized Linear Model fit statistics for supervised PCA 

Extract and test principal components from supervised PCA 

Train a supervised PCA model 

Singular Value Decomposition wrapper for supervised PCA 

Calculate the optimal parameters for a mixture of Weibull Extreme Value Distributions for supervised PCA 

Calculate the \(p\)values from an optimal mixture of Weibull Extreme Value distributions for supervised PCA 

Calculate pathwayspecific Student's \(t\)scores from a null distribution for supervised PCA 

Calculate pathwayspecific Student's \(t\)scores for supervised PCA 

Internal Supplemental FunctionsUtility functions shared by both the AESPCA and supervised PCA methods or CreateOmics 


Generation functions for 
Delete Ome symbols or IDs without matching features recorded in a given assay data frame from a pathway collection 

Tabulate, adjust, and sort pathway \(p\)values 

Adjust \(p\)values for simple multipletesting procedures 

Parametric bootstrap and nonparametric permutations of a response vector or matrix 