simulateT1: One update step in simulation

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

One update step in simulation

Description

This function does one update step in a simulation process

Usage

simulateT1(nodes.t=nodes.t,intermediates.AND=intermediates.AND,integrators.AND=integrators.AND,intm.inN=intm.inN,intg.inN=intg.inN,sink.inN=sink.inN)

Arguments

nodes.t	numeric matrix with two columns being the state of each node at state t and state t+1, status of nodes are 0 or 1
intermediates.AND	for each intermediate in the network, this is a logical that says if inputs enter it with an AND gate or not
integrators.AND	for each integrator in the network, this is a logical that says if inputs enter it with an AND gate or not. This is NA if the integrators are not considered as intermediates
intm.inN	a list with an entry for each intermediate that has inputs, containing a character vector with the names of input nodes of the node
intg.inN	a list with an entry for each integrator that has inputs, containing a character vector with the names of input nodes of the node
sink.inN	a list with an entry for each sink that has inputs, containing a character vector with the names of input nodes of the node

Details

This function computes the status of each node (recorded in column 2 of nodes.T) at t+1 as a function of the status of its parents at t (column 1) according to a model

Value

the updated nodes.t matrix

Author(s)

C. Terfve

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