sismonr (version 2.1.0)

addGene: Adds a gene in the in silico system.

Description

Adds a gene in the in silico system with specified parameters if provided, or with parameters sampled according to the system parameters.

Usage

addGene(
  insilicosystem,
  coding = NULL,
  TargetReaction = NULL,
  TCrate = NULL,
  TLrate = NULL,
  RDrate = NULL,
  PDrate = NULL
)

Arguments

insilicosystem

The in silico system (see createInSilicoSystem).

coding

String. The coding status of the gene (either "PC" for protein-coding or "NC" for noncoding). If none provided, randomly chosen according to the parameter PC.p provided in sysargs (see insilicosystemargs).

TargetReaction

String. The biological function of the gene, i.e. the gene expression step targeted by the active product of the gene. If none provided, randomly chosen according to the parameters PC.TC.p, etc or NC.TC.p, etc (depending on the coding status of the gene) provided in sysargs (see insilicosystemargs).

TCrate

Numeric. The transcription rate of the gene. If none provided, randomly chosen according to the parameter basal_transcription_rate_samplingfct provided in sysargs (see insilicosystemargs).

TLrate

Numeric. The translation rate of the gene. If none provided, randomly chosen according to the parameter basal_translation_rate_samplingfct provided in sysargs (see insilicosystemargs).

RDrate

Numeric. The RNA decay rate of the gene. If none provided, randomly chosen according to the parameter basal_RNAlifetime_samplingfct provided in sysargs (see insilicosystemargs).

PDrate

Numeric. The protein decay rate of the gene. If none provided, randomly chosen according to the parameter basal_protlifetime_samplingfct provided in sysargs (see insilicosystemargs).

Value

The modified in silico system.

Examples

# NOT RUN {
mysystem = createInSilicoSystem(G = 5)
mysystem$genes
mysystem2 = addGene(mysystem, "PC", "TC", TCrate = 0.0001, TLrate = 0.001)
mysystem2$genes

mysystem3 = addGene(mysystem2)
mysystem3$genes
# }