run1model: Creates and runs 1 model

In saezlab/PHONEMeS-ILP: Building logic-based models from discovery high-content phosphoproteomics data

Creates and runs 1 model

Description

This function creates a model, simulates it and outputs its score, given a data set

Usage

run1model(pknList=pknList, targetsOn=targets.P,dataOn=data.P,FlipP=rep(0.5, length(intermediates(pknList))),AndBinF=rep(0, length(integrators(pknList))),NoneBinF=rep(0, length(integrators(pknList))),dataGMM=dataGMM,optParam)

Arguments

pknList	a PKNlist object
optParam	cstart (logical, should the interactionsD set of interactions be added to every model, normally only set to TRUE at generation 1), and intgAsintm (logical, should integrators be treated like intermediates)
targetsOn	a list of string vectors containing the UPIDs of kinases hit by each set of drugs
dataOn	a GMMbyCond object
FlipP	a numeric vector, the probability of AND for each intermediate
AndBinF	a numeric vector, either an integer giving the number of bins for the AND gate of each integrator (if intgAsintm(optParam)=FALSE), or the probability of AND for each integrator (if intgAsintm(optParam)=TRUE)
NoneBinF	a numeric vector (of the same length as the number of integrator nodes), the number of bins for the no-gate option, for each integrator node
dataGMM	a GMMres object

Value

a list with elements: model (the model, as created by createModel, score (the score of the model), scoresList (a list of scores in the same format as dataOn but with a single numeric value in each element, which is the score produced by the data under that drug), intAnd/intgAnd (a logical vector for each intermediate/integrator: AND or OR gated). AndBinF and NoneBinF are NA if intgAsintm is TRUE (deprecated).

Author(s)

C. Terfve

saezlab/PHONEMeS-ILP documentation built on June 21, 2022, 5:36 p.m.