gep2pep-package | gep2pep: creation and analysis of Pathway Expression Profiles |
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 |