Man pages for molsysbio/STASNet
Fit and Simulate Model from Perturbation Data
| addLayerLinks | Generate a list of links between two layers with a... |
| addLink | add Link routine |
| addPLinfos | Add the information provided by the profile likelihood in the... |
| addVariableParameters | Search for and relax fixed coefficients of an MRAmodelSet to... |
| aggregateDirectPaths | Aggregate the paths values for plotting |
| cloneModel | Clone an MRAmodel or MRAmodelSet object |
| compareParameters | Compare networks |
| computeFitScore | Compute the fitting scores of a model |
| controlFC | Compute the log-fold change to control |
| createDataSet | Import multiple files to create a group of models |
| createModel | Creates and fits a parameterised model from experimental... |
| createModelSet | Build an MRAmodelSet |
| createSimulation | Create simulated data |
| exportModel | Exports the model in a file |
| extraction | Extraction of object from file or object |
| extractModelCore | Extracts the data, the experimental design and the structure... |
| extractSubmodels | Extract individual models from an MRAmodelSet |
| fitmodel | Fit and simulate model from perturbation data |
| generate_infos | Build infos vector from the parameters used to build the... |
| generateToyDesign | Generate an experimental design for a toy network |
| generateToyNetwork | Generate a fake network tab file |
| getCombinationMatrix | Create a perturbation matrix |
| getDirectPaths | Compute direct paths for a model |
| getModelError | Compute the error of the model |
| getParametersNames | Return the paths corresponding to each parameter |
| getSamples | Get LHS samples |
| getSimulation | Simulate the model for the experimental design used for the... |
| importModel | Import model from a file |
| initModel | Perform an initialisation of the model |
| midasFromData | Write a MIDAS file from a human readable dataset |
| modelGroup | Constructor for modelGroup objects |
| MRAmodel | Constructor for MRAmodel objects |
| MRAmodelSet | Constructor for MRAmodelSet objects |
| mul_path | Multiply two paths (list of links with exponent) |
| niplotPL | Plots the functional relations between each non-identifiable... |
| plotHeatmap | Plot a customized heatmap with a symmetrical scale that is... |
| plotModelAccuracy | Plot heatmaps of the model simulation against the data... |
| plotModelGraph | Plot the network used in the model |
| plotModelParameters | Plot the parameters for a model or a list of models |
| plotModelScores | Plot the fitting scores of the model |
| plotModelScores.modelGroup | Plot the measurement scores for a group of models |
| plotModelScores.MRAmodel | Plot the scores of each antibody |
| plotModelSimulation | Plot the predictions by the model |
| plotNetworkGraph | Plot a graph from an adjacency list |
| plotParameters | Plot parameters |
| plotParameters.modelGroup | Plot the parameters of the models |
| plotResiduals | Plot the residual of each model in the group |
| plotSimulation | Plot predictions generated by simulateModel One plot per... |
| printParameters | Print the value of the parameters of the model |
| profileLikelihood | Computes the profile likelihood and the parameter... |
| readMIDAS | Read a MIDAS file |
| readNetworkAdj | Get an adjacency matrix from a file |
| rebuildModel | Import a saved model with data files |
| rebuildModelSet | Import a saved set of models with data files to construct a... |
| refit | Fit a model using the parameter set from another model |
| refitWithFixedParameter | Refit modelset by iterative lumping of variable parameters... |
| refitWithVariableParameter | Refit modelset by iterative relaxation of single parameters |
| selectMinimalModel | Selection of a minimal model by iteratively removing... |
| setVariableParameters | Set the variable parameters of a modelset |
| simulateModel | Get the target simulations in a MIDAS design-like or list... |
| sub_data_frame | Return a data.frame even if the output as on line or one... |
| suggestExtension | Tries to locally add one link each and returns a list of... |
| testModel | Computes the fitting scores for a new parameter set |
