Man pages for franapoli/gep2pep
Creation and Analysis of Pathway Expression Profiles (PEPs)

as.CategorizedCollectionConverts GeneSetCollection objects to CategorizedCollection...
buildPEPsBuild PEPs from GEPs and stores them in the repository.
CategorizedCollectionConstructor method for objects of class...
CategorizedCollection-classA class to contain categorized gene set collection
checkRepositoryCheck an existyng repository for consistency
clearCacheClear cached ranked matrices
CondSEAPerforms Condition Set Enrichment Analysis
createMergedRepositoryMerge multiple PEPs to build a repository of consensus PEPs
createRepositoryCreates a repository of pathway collections.
exportSEAExport CondSEA or PathSEA results to XLS format
gene2pathwaysFinds pathways including a given gene.
gep2pep-packagegep2pep: creation and analysis of Pathway Expression Profiles
getCollectionsReturns the names of the pathway collections in a repository.
getDetailsExtracts the details matrix from 'CondSEA' or 'PathSEA'...
getResultsExtracts the results matrix from 'CondSEA' or 'PathSEA'...
importFromRawModeImports PEPs created in raw mode
importMSigDB.xmlImports pathways data from an MSigDB XML file.
loadCollectionLoads a collection of pathways from the repository
loadESmatrixLoads the matrix of Enrichment Scores for a collection
loadPVmatrixLoads the matrix of p-values for a collection
loadSampleGEPLoads sample Gene Expression Profiles
loadSamplePWSLoads sample pathway collections
makeCollectionIDsCreates a collection label for each pathway.
openRepositoryOpens an existing repository of pathway collections.
PathSEAPerforms Pathway Set Enrichment Analysis (PSEA)
setId2setNameConverts gene set IDs to gene set names
franapoli/gep2pep documentation built on May 16, 2018, 8:33 p.m.