createGenes: Creates genes for the in silico system.

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

Creates genes for the in silico system.

Description

Generates the genes in the system and their attributes, according to the user parameters.

Usage

createGenes(sysargs)

Arguments

sysargs

An object of class insilicosystemargs (i.e. a list with parameters for in silico system generation).

Value

A data frame of in silico genes. Attributes:

• id: Integer, ID of the genes;

• coding: coding status of the genes (either "PC" for protein-coding or "NC" for noncoding). Sampled according to the parameter PC.p in sysargs;

• 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). Sampled according to the parameters PC.TC.p, etc for protein-coding genes or NC.TC.p, etc for noncoding genes, in sysargs;

• PTMform: Does the gene have a PTM form? "0" or "1" (here all "0", PTM form will be assigned later);

• 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. Sampled according to the parameter

  basal_transcription_rate_samplingfct in sysargs;

• TLrate: translation rate of the genes. Sampled according to the parameter

  basal_translation_rate_samplingfct in sysargs (0 for noncoding genes);

• RDrate: RNA decay rate of the genes. Sampled according to the parameter

  basal_RNAlifetime_rate_samplingfct in sysargs;

• PDrate: Protein decay rate of the genes. Sampled according to the parameter

  basal_protlifetime_rate_samplingfct in sysargs (0 for noncoding genes).

Examples

createGenes(insilicosystemargs(G = 5))

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