Creation and Analysis of Pathway Expression Profiles (PEPs)

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Documentation for package ‘gep2pep’ version 1.29.0

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

Help Pages

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