Man pages for franapoli/gep2pep
Creation and Analysis of Pathway Expression Profiles (PEPs)
| addSingleGeneSets | Adds a collection of single-gene psuedo-sets. |
| as.CategorizedCollection | Converts GeneSetCollection objects to CategorizedCollection... |
| buildPEPs | Build PEPs from GEPs and stores them in the repository. |
| CategorizedCollection | Constructor method for objects of class... |
| 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-package | 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'... |
| getResults | Extracts the results matrix from 'CondSEA' or 'PathSEA'... |
| 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 |
