BMsim: Create and simulate a model

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

Create and simulate a model

Description

This function creates a pruned model and the simulation matrix associated with it

Usage

BMsim(BM, nodes2link, BM.intAnd, pknList, targetsOn)

Arguments

BM	a model data frame, i.e. a subset of a background model data frame (interactions(pknList)), that only contains those edges that are present in this particular model
BM.intAnd	a logical vector of the same length as the number of intermediates, that has the intermediates AND status associated with the model at hand
nodes2link	a character vector of names of those nodes that we are trying to reach (i.e. they match nodes in the S.cc column of the background network, and should normally be data nodes, although they don't have to be)
pknList	A PKNlist object
targetsOn	a list of drugs targets, matching to the conditions in the data as stored in the GMMbyCond object (i.e. one element of this list contains the K/P affected under one condition, which itself can match to multiple drug treatments with identical targets).

Value

a list with two elements

BM.nopathR	a model data frame with edges that cannot be connected to a data node removed
BM.sim	a simulation matrix that has a row for each node and a column for each condition (set of perturbed kinases, possibly matching to multiple experimental treatments with the same affected K/P), x.ij=0 if node i is not perturbed under condition j, and 1 if it is perturbed.

Author(s)

C. Terfve

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