runDynamicFeeder: Modelling the integrated PKN with CNORode

In saezlab/CNORfeeder: Integration of CellNOptR to add missing links

Modelling the integrated PKN with CNORode

Description

This function evaluates the effects of possible feeder mechanisms which are added to the PKN.

Usage

runDynamicFeeder(cnolist = cnolist, integratedModel = integratedModel, ode_parameters = ode_parameters, penFactor_k = 100, penFactor_tau = 1, penFactorPIN_k = 10, paramsSSm = defaultParametersSSm())

Arguments

cnolist	a cnolist structure, as produced by makeCNOlist
integratedModel	the integrated model as returned from integrateLinks
ode_parameters	a list with the ODEs parameter information.
penFactor_k	a penalty factor for the new integrated links obtained from the FEED algorithm and which are not present in the database (if the database was given). Default: penFactor_k = 100
penFactor_tau	a penalty factor for all the new nodes integrated in the PKN. Default: penFactor_tau = 1
penFactorPIN_k	a penalty factor for the new integrated links and which are present in the database (for the cases when the database was given). Default: penFactorPIN_k = 10
paramsSSm	a list of SSm parameters. default is the list returned by defaultParametersSSm

Details

This function evaluates the effects of possible feeder mechanisms which are added to the PKN. The analysis performed is a simple CNORode analysis over the integrated network where the newly integrated links are supposed to be penalised more than the links present in the original PKN. If a database of interactions is also provided by the user, than normally the links inferred from the FEED mechanism and which re not present in the database should be more penalised than the ones that are. There is also the opportunity to weight database interactions based on their relevance (i.e. number of resources, etc.).

Value

this function returns a list with fields:

Parameters	the inferred optimal ODE parameters
Integrated-Model	the integrated model which was optimised
CNOlist	the CNOlist object containing the data

Author(s)

E.Gjerga

Examples

data(integratedModel_toy, package="CNORfeeder")
data(CNOlistToy_Gene, package="CNORfeeder")
data(simData_toy,package="CNORfeeder")


## To be run with the recent version of the CNORode package: 
## https://github.com/saezlab/CNORode
# 
# library(CNORode)
# 
# paramsSSm=defaultParametersSSm()
#
# ode_parameters=createLBodeContPars(integratedModel$model, LB_n = 1, LB_k = 0,
#                                    LB_tau = 0, UB_n = 3, UB_k = 1, UB_tau = 1, default_n = 3,
#                                    default_k = 0.5, default_tau = 0.01, opt_n = FALSE, opt_k = TRUE,
#                                    opt_tau = TRUE, random = TRUE)
#                                    
# result = runDynamicFeeder(cnolist = cnolist, integratedModel = integratedModel,
#                           ode_parameters = ode_parameters, paramsSSm = paramsSSm,
#                           penFactor_k = 2, penFactorPIN_k = 0.1, penFactor_tau = 1)
#                               

saezlab/CNORfeeder documentation built on Feb. 14, 2023, 3:23 p.m.