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| FELLA-package | The FELLA package |
| addGOToGraph | Generate and manipulate tables and sub-networks from an enrichment |
| buildDataFromGraph | Parse, build and load the KEGG knowledge model |
| buildGraphFromKEGGREST | Parse, build and load the KEGG knowledge model |
| D.diffusion-class | An internal S4 class for the diffusion data |
| D.hypergeom-class | An internal S4 class for the binary matrix (hypergeometric test) |
| D.keggdata-class | An internal S4 class to represent the KEGG graph and related files |
| D.pagerank-class | An internal S4 class for the PageRank data |
| data-funs | Parse, build and load the KEGG knowledge model |
| defineCompounds | Functions to map and enrich a list of metabolites |
| enrich | Functions to map and enrich a list of metabolites |
| enrich-funs | Functions to map and enrich a list of metabolites |
| export-funs | Generate and manipulate tables and sub-networks from an enrichment |
| exportResults | Generate and manipulate tables and sub-networks from an enrichment |
| FELLA | The FELLA package |
| FELLA.DATA | An S4 class to represent all the necessary KEGG data |
| FELLA.DATA-class | An S4 class to represent all the necessary KEGG data |
| FELLA.sample | FELLA.DATA sample data |
| FELLA.USER | An S4 class to save all the user analysis data |
| FELLA.USER-class | An S4 class to save all the user analysis data |
| generateEnzymesTable | Generate and manipulate tables and sub-networks from an enrichment |
| generateResultsGraph | Generate and manipulate tables and sub-networks from an enrichment |
| generateResultsTable | Generate and manipulate tables and sub-networks from an enrichment |
| getBackground | Get compounds in the defined background |
| getCom | Get community |
| getExcluded | Get excluded compounds |
| getGraph | Get KEGG graph |
| getInfo | Get KEGG version info |
| getInput | Get metabolites in the input |
| getMatrix | Get matrix for the desired methodology |
| getName | Map KEGG identifiers to KEGG names |
| getPscores | Get p-scores from the desired methodology |
| getStatus | Get the slot "status" |
| getSums | Get rowSums/squaredRowSums |
| getValid | Get the slot "valid" |
| input.sample | A randomly generated list of affected metabolites |
| is.FELLA.DATA | Check FELLA.DATA class |
| is.FELLA.USER | Check FELLA.USER class |
| launchApp | Launch a shiny app with FELLA |
| listApprox | List of approximations |
| listCategories | List of node categories |
| listInternalDatabases | List internal databases |
| listMethods | List of methods |
| loadKEGGdata | Parse, build and load the KEGG knowledge model |
| plot-method | An S4 class to save all the user analysis data |
| plotGraph | Generate and manipulate tables and sub-networks from an enrichment |
| plotLegend | Internal function to add a legend to a graph plot |
| runDiffusion | Functions to map and enrich a list of metabolites |
| runHypergeom | Functions to map and enrich a list of metabolites |
| runPagerank | Functions to map and enrich a list of metabolites |
| show-method | An S4 class to represent all the necessary KEGG data |
| show-method | An S4 class to save all the user analysis data |
| U.diffusion-class | An internal S4 class for the user data of the diffusion enrichment analysis |
| U.hypergeom-class | An internal S4 class for the user data of the hypergeometric over representation analysis |
| U.pagerank-class | An internal S4 class for the user data of the PageRank enrichment analysis |
| U.userinput-class | An internal S4 class for the user input data |