Man pages for b2slab/FELLA
Interpretation and enrichment for metabolomics data
| checkArguments | Internal function to check arguments and give personalised... |
| data-funs | Parse, build and load the KEGG knowledge model |
| D.diffusion | An internal S4 class for the diffusion data |
| D.hypergeom | An internal S4 class for the binary matrix (hypergeometric... |
| D.keggdata | An internal S4 class to represent the KEGG graph and related... |
| dot-params | Dummy function with function arguments |
| D.pagerank | An internal S4 class for the PageRank data |
| enrich-funs | Functions to map and enrich a list of metabolites |
| export-funs | Generate and manipulate tables and sub-networks from an... |
| FELLA | The FELLA package |
| FELLA.DATA | 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 |
| 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 |
| getPvaluesSize | Get matrix for the p-value regarding CC size |
| getStatus | Get the slot "status" |
| getSums | Get rowSums/squaredRowSums |
| getValid | Get the slot "valid" |
| infere.con2ec | Infer connections to EC |
| input.sample | A randomly generated list of affected metabolites |
| is.FELLA.DATA | Check FELLA.DATA class |
| is.FELLA.USER | Check FELLA.USER class |
| largestcc | Extract largest CC |
| launchApp | Launch a shiny app with FELLA |
| listApprox | List of approximations |
| listCategories | List of node categories |
| listInternalDatabases | List internal databases |
| listMethods | List of methods |
| mytriangle | Add triangular shape to igraph plot |
| plotBipartite | Internal function to plot a bipartite graph |
| plotLegend | Internal function to add a legend to a graph plot |
| sanitise | ID sanitiser function |
| U.diffusion | An internal S4 class for the user data of the diffusion... |
| U.hypergeom | An internal S4 class for the user data of the hypergeometric... |
| U.pagerank | An internal S4 class for the user data of the PageRank... |
| U.userinput | An internal S4 class for the user input data |
