PKNlist: Create a 'PKNlist' object

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

Create a PKNlist object

Description

This function creates a PKNlist object which contains all the elements based on a background network as created by buildPKN, that are needed for the optimisation

Usage

PKNlist(PKN, targets.On, data.On)

Arguments

PKN	a KPSbg object created by buildPKN
targets.On	a list of drug targets (as character vectors) by condition, matching to the data.On object
data.On	a GMMbyCond object as created by dataBycond

Value

a PKNlist object with elements interactions (a condensed form of the version in the original network in the object created by buildPKN, that aggregates identical interactions from multiple sources, with weights modified accordingly), interactionsD (a subset of interactions that only contains experimentally supported direct interactions between data points and drug targets), intermediates (a character vector of intermediate nodes), sinks (a character vector of sink nodes), integrators (a character vector of integrator nodes).

Author(s)

C. Terfve

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