simulateModel: Get the target simulations in a MIDAS design-like or list...
In MathurinD/STASNet: Fit and Simulate Model from Perturbation Data

Description Usage Arguments Value See Also

Get the target simulations in a MIDAS design-like or list format Simulate a model for a specified set of perturbation

1 2	simulateModel(model_description, targets = "all", readouts = "all", inhibition_effect = NA, with_offset = TRUE)

`model_description`	A MRAmodel object that describes the model to be fitted
`targets`	A matrix of perturbations to simulate, as generated by getCombinationMatrix or "all" to reproduce the perturbations used to build the model A perturbation matrix is filled with 0 and 1, each row is a perturbation set and column names are used to determine the name of the perturbation.
`readouts`	List of nodes to simulate. If "all", all the nodes measured to fit the model will be used. Only nodes actually measured or inhibited for the model can be simulated.
`inhibition_effect`	A single value, a list of values or NA. Values in ]0, -inf] to use for the inhibition, representing the log2-fold change in activity of the node (alternatively, a value between 0 and 1 representing the fraction of activity remaining after inhibition compared to basal). If NA, the values fitted for the inhibition will be used, or -1 if an inhibition is requested for a node that was not inhibited in the experiment.
`with_offset`	Whether the simulation should include the offset (fitted simulation) or not (real activity prediction)

A list that represents a MIDAS measure-like format with fields 'conditions' the matrix of perturbations provided as 'targets', 'bestfit' the simulation, and 'variants' a list of simulations for the alternative parameter sets from profile likelihood

Other simulation: getCombinationMatrix, plotSimulation

MathurinD/STASNet documentation built on May 28, 2019, 1:50 p.m.