createMultiOmicNetwork: Creates an in silico system.

In oliviaAB/sismonr: Simulation of in Silico Multi-Omic Networks

Creates an in silico system.

Description

Creates an in silico system from a data-frame of genes in the system.

Usage

createMultiOmicNetwork(genes, sysargs, ev = getJuliaEvaluator())

Arguments

genes	A data-frame of the genes existing in the system (see createGenes).
sysargs	An object of class insilicosystemargs (i.e. a list with parameters for in silico system generation).
ev	A Julia evaluator. If none provided select the current evaluator or create one if no evaluator exists.

Value

An in silico system, that is a list of:

• genes: the modified data-frame of genes;

• edg: A data-frame of edges in the regulatory network of the system (1 row = 1 edge). It contains the following parameters:

  • from: gene ID of the edge origin (character).

  • to: gene ID of edge destination (character).

  • TargetReaction: Type of regulation (ID of the controlled reaction: "TC", "TL", "RD", "PD" or "PTM").

  • RegSign: Sign of the reaction ("1" for positive regulation, "-1" for negative regulation).

  • RegBy: Type of the regulator: "PC" for protein-coding regulation, "NC" for noncoding regulator, "C" for regulatory complex.

• mosystem: A list of the different regulatory networks (each corresponding to a different type of regulation) in the system and associated information. Elements are TCRN_edg, TLRN_edg, RDRN_edg, PDRN_edg and PTMRN_edg: data-frames of edges for the different regulatory networks, which in addition to the usual fields in the edg data frame, contain columns for kinetic parameters of the regulation.

• complexes: a list of regulatory complexes composition. The names of the elements are the IDs of the complexes, and the values are vectors of gene IDs constituting each regulatory complex.

• complexeskinetics: a list of regulatory complexes kinetic parameters.

• complexesTargetReaction: a list defining which expression step is targeted by each regulatory complex.

Examples

## Not run: 
mysysargs = insilicosystemargs(G = 5)
mygenes = createGenes(mysysargs)
mynetwork = createMultiOmicNetwork(mygenes, mysysargs)

## End(Not run)

oliviaAB/sismonr documentation built on June 25, 2022, 11:59 p.m.