sracipeConvergeDist: A method to visualize convergence distributions

In lusystemsbio/sRACIPE: Systems biology tool to simulate gene regulatory circuits

A method to visualize convergence distributions

Description

When convergence tests are done (deterministic systems with time series off), this method creates a plot of the proportion of converged initial conditions as the number of convergence tests increases, up to the total number done by the simulation. Note that when limit cycles are detected, they are automatically removed from consideration. This method also adds some statistics to the metadata of the input. Models with NaN values are also removed. Specifically, the final proportion of converged states is reported, and if it exists, the smallest number of convergence tests where at least 99 percent of models converged is also reported.

Usage

sracipeConvergeDist(.object, plotToFile = FALSE)

## S4 method for signature 'RacipeSE'
sracipeConvergeDist(.object, plotToFile = FALSE)

Arguments

.object	RacipeSE object generated by sracipeSimulate function.
plotToFile	(optional) logical. Default FALSE. Whether to save plots to a file.

Value

RacipeSE object

Related Functions

sracipeSimulate, sracipeKnockDown, sracipeOverExp, sracipePlotData

Examples

data("demoCircuit")
## Not run: 
rSet <- sRACIPE::sracipeSimulate(circuit = demoCircuit, numModels = 20,
integrateStepSize = 0.1, numConvergenceTests = 30)
rSet <- sracipeConvergeDist(rSet)

## End(Not run)

lusystemsbio/sRACIPE documentation built on Nov. 19, 2024, 9:07 a.m.