createGenes: Creates genes for the in silico system.

In sismonr: Simulation of in Silico Multi-Omic Networks

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))

sismonr documentation built on Feb. 11, 2020, 9:07 a.m.