getGenes: Retrieve genes from in silico system

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

Retrieve genes from in silico system

Description

Returns a data-frame of the genes and associated properties in the in silico system.

Usage

getGenes(insilicosystem)

Arguments

insilicosystem

The in silico system (see createInSilicoSystem).

Value

A data-frame with the following columns:

• id: Integer, ID of the genes;

• coding: coding status of the genes (either "PC" for protein-coding or "NC" for noncoding);

• TargetReaction: the biological function of the genes ("TC": transcription regulator, "TL": translation regulator, "RD": RNA decay regulator, "PD": protein decay regulator, "PTM": post-translational modification regulator, "MR": metabolic enzyme);

• PTMform: Does the gene have a PTM form?

• Active form: what is the active form of the gene? "R" for noncoding genes, "P" for protein-coding genes, "Pm" for protein-coding genes with a PTM form;

• TCrate: transcription rate of the genes;

• TLrate: translation rate of the genes;

• RDrate: RNA decay rate of the genes;

• PDrate: Protein decay rate of the genes.

Examples

## Not run: 
mysystem = createInSilicoSystem(G = 10)
getGenes(mysystem)

## End(Not run)

oliviaAB/sismonr documentation built on Jan. 26, 2025, 10:20 a.m.