OptParam-class: PHONEMeS analysis parameters

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

PHONEMeS analysis parameters

Description

This class contains all parameters for an analysis

Objects from the Class

Objects of class OptParam can be created from new("OptParam", sizeP=0, nG1=100, cstart=TRUE, intgAsintm=FALSE, nScripts=50, absTol=FALSE, tol=0.15, cap=20, resN=2, nG=50)

Slots

sizeP:

numeric, size penalty factor

nG1:

numeric, number of models sampled in each script

cstart:

logical, should the direct interactions between drug targets and data sites be added to every model

intgAsintm:

logical, TRUE if we want integrators to be sampled the same way intermediates are

nScripts:

numeric, number of parallel scripts that are run at each generation

absTol:

logical, should absolute tolerance be used

tol:

numeric, tolerance

cap:

numeric, maximum number of times that an edge is copied through at each generation

resN:

index of the optimisation (for naming files and folders)

nG:

number of generations that the optimisation is run for

Methods

An overview of methods with class-specific functionality: More detailed introduction can be found in help for each specific function.

Author(s)

C. Terfve [e-mail]

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