Man pages for saezlab/PHONEMeS-ILP
Building logic-based models from discovery high-content phosphoproteomics data
| assignAttributes | Assigning node attributes |
| BMsim | Create and simulate a model |
| buildInputs | Function to generate the data inputs of PHONEMeS |
| buildNw | Make a starting network object |
| buildPKN | Make a starting network |
| createModel | Sample a candidate model |
| dataBycond | Function that re-shapes the data so that its entries match... |
| dataTable | Create a data table for sites in a network |
| GMMbyCond-class | Processed MS data, organised by condition |
| GMMres-class | Processed MS data |
| integratorWeights | Integrator weights correction |
| intermediateWeights | Correction to intermediate weights |
| mInw | Create maximum input network |
| ModelList-class | Sampled models and scores |
| nodeAttr | Writes node attributes for a network and data set |
| nodesData | Nodes On/Off in a network, given some data |
| OptParam-class | PHONEMeS analysis parameters |
| oRes | Import and combine optimisation results |
| pathsD | Max scoring path |
| PHONEMeS-package | MS phosphoproteomics-based models of signalling |
| PKNlist | Create a 'PKNlist' object |
| PKNlist-class | K/P-S network |
| plotoRes | Produces optimisation diagnostic plots |
| run1model | Creates and runs 1 model |
| runLimma | Function to perform differential analysis with Limma |
| runPHONEMeS | Function to run PHONEMeS-ILP |
| runPHONEMeS_Downsampling | Function to run PHONEMeS-ILP. Similar to runPHONEMeS, however... |
| runPHONEMeS_mult | Function to run the PHONEMeS-ILP method for time-resolved... |
| runPHONEMeS_UD | Function to run the upside-down variant of PHONEMeS |
| simulateT1 | One update step in simulation |
| sinkWeights | Sinks weight correction |
