Creation and Analysis of Pathway Expression Profiles (PEPs)

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Documentation for package ‘gep2pep’ version 1.10.0

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gep2pep-package gep2pep: creation and analysis of Pathway Expression Profiles
addSingleGeneSets Adds a collection of single-gene psuedo-sets.
as.CategorizedCollection Converts GeneSetCollection objects to CategorizedCollection objects.
buildPEPs Build PEPs from GEPs and stores them in the repository.
CategorizedCollection Constructor method for objects of class CategorizedCollection.
CategorizedCollection-class A class to contain categorized gene set collection
checkRepository Check an existyng repository for consistency
clearCache Clear cached ranked matrices
CondSEA Performs Condition Set Enrichment Analysis
createMergedRepository Merge multiple PEPs to build a repository of consensus PEPs
createRepository Creates a repository of pathway collections.
exportSEA Export CondSEA or PathSEA results to XLS format
gene2pathways Finds pathways including a given gene.
gep2pep gep2pep: creation and analysis of Pathway Expression Profiles
getCollections Returns the names of the pathway collections in a repository.
getDetails Extracts the details matrix from 'CondSEA' or 'PathSEA' output
getResults Extracts the results matrix from 'CondSEA' or 'PathSEA' output
importFromRawMode Imports PEPs created in raw mode
importMSigDB.xml Imports pathways data from an MSigDB XML file.
loadCollection Loads a collection of pathways from the repository
loadESmatrix Loads the matrix of Enrichment Scores for a collection
loadPVmatrix Loads the matrix of p-values for a collection
loadSampleGEP Loads sample Gene Expression Profiles
loadSamplePWS Loads sample pathway collections
makeCollectionIDs Creates a collection label for each pathway.
openRepository Opens an existing repository of pathway collections.
PathSEA Performs Pathway Set Enrichment Analysis (PSEA)
setId2setName Converts gene set IDs to gene set names