createModel: Sample a candidate model

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

Sample a candidate model

Description

This function samples an interaction object (PKNlist) to make a candidate model

Usage

createModel(pknList=pknList,AndBinF=rep(1, length(integrators(pknList))),NoneBinF=rep(1, length(integrators(pknList))),optParam=optParam)

Arguments

pknList	a PKNlist object produced by buildPKN, with elements interactions (an interaction data frame), sinks (a character vector of sink nodes), species (a character vector of nodes), interactionsD (a subset of interactions that only contains experimentally supported direct interactions between drug targets and data points), intermediates (a character vector of intermediate nodes), integrators (a character vector of integrator nodes)
AndBinF	a numeric vector of the same length as the number of integrators
NoneBinF	a numeric vector of the same length as the number of integrators
optParam	an OptParam object with at least the elements intgAsintm (logical, TRUE if we want integrators to be sampled the same way intermediates are) and cstart (logical, should the interactionsD set of interactions be added to every model)

Value

a data frame of interactions that is a subset of the interactions in interactions(pknList)

Author(s)

C. Terfve

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