Man pages for cmujzbit/OmicsON
OmicsON is a package implementing workflow for finding associations acrossomics data sets
| clusterUsingOntology | OmicsON - private function. |
| createFunctionalInteractionsDataFrame | Create a functional interactions data frame. |
| decorateByReactomeData | Decorate data by data presented in Reactome database. |
| decorateByStringDbData | Decorate data from previous step (Reactome decoration) by... |
| firstExistsInReactomeChebiOntology | OmicsON - private function. |
| getStringNeighbours | OmicsON - private function. |
| getSymbolsBaseOnEnsemblPeptidIdsUsingMyGenePackage | OmicsON - private function. |
| makeCanonicalCorrelationAnalysis | Calculate CCA on data returned from decoration methods. |
| makeCCAOnGroups | OmicsON - private function. |
| makePartialLeastSquaresRegression | Calculate PLS on data returned from decoration methods. |
| makePermutationTestOnCCA | OmicsON - private function. |
| makePermutationTestOnPLS | OmicsON - private function. |
| makePLSOnGroups | OmicsON - private function. |
| mapFromStringIdsToEnsembleIds | OmicsON - private function. |
| mapReactomePathwaysUnderOrganism | OmicsON - private function. |
| mergeChEBIOntologyWithChildFavoring | OmicsON - private function. |
| plotCanonicalCorrelationAnalysisResults | Plot CCA analysis results. |
| plotRegression | Plot PLS analysis results. |
| plotRmsepForPLS | Plot RMSEP for PLS analysis results. |
| readGroupsAsDf | OmicsON - private function. |
| setUpReactomeMapping | Set up space of mappings in package. |
