| calculate_TemporalGSSA {TemporalGSSA} | R Documentation |
calculate_TemporalGSSA() This is the main function of the package 'TemporalGSSA'.
Description
'TemporalGSSA', may be considered a wrapper for the R-package 'GillespieSSA'. The formatted data generated by consecutive runs of 'GillespieSSA' for molecules of a generic biochemical network will generate a dataset of randomly chosen timesteps along with changes to the corresponding number of molecules. This constitutes a set observations for a specific simulation time.
Usage
calculate_TemporalGSSA(data, type, out)
Arguments
data |
Formatted data from the output of consecutive 'GillespieSSA' runs. This is a mandatory argument. |
type |
A mandatory integer argument that indicates the statistic that will be used to compute the representative timestep for a set of observations. Here: "1" is the MEAN, "2" is the MEDIAN, "3" is a random choice and "4" is ALL |
out |
An optional logical argument that control the console output with default being "TRUE" Here, TRUE curtails the output while FALSE allows the verbose output of all the coefficents . |
Details
The temporal profile of a metabolite is a pre-requisite to comprehend its behaviour in vivo.
This is accomplished by transforming the raw formatted data into a metabolite-specific trial. Each such trial is defined as a set of linear models (n >= 30) between a timestep and number of molecules for a metabolite. The coefficients of these models (slope, constant) are averaged and incorporated into a metabolite-specific linear regression model. The independent variable is a representative timestep and is user-dependent. The generated data is an imputed number of molecules for each metabolite, is dependent on the simulation time and is defined as a "technical replicate".
The above steps are easily repeated with additional SSA-runs (n >=30) and will generate sets of "technical replicates". These can be statistically evaluated (mean, standard deviation) and will constitute the simulation time-dependent number of molecules for a particular metabolite. For varying simulation times 'TemporalGSSA' will generate a metabolite-specific and simulation time-dependent trajectory.
Value
code A numerically encoded ('0', success; '1', no success) text message to the user indicating the outcome of "TemporalGSSA".
The examples listed below can be run directly from the console as example("calculate_TemporalGSSA")
Examples
calculate_TemporalGSSA(valid,1)
calculate_TemporalGSSA(valid,4)
calculate_TemporalGSSA(nvalid,2)