Generates the genes in the system and their attributes, according to the user parameters.
An object of class
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
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
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
TLrate: translation rate of the genes. Sampled according to the parameter
sysargs (0 for noncoding genes);
RDrate: RNA decay rate of the genes. Sampled according to the parameter
PDrate: Protein decay rate of the genes. Sampled according to the parameter
sysargs (0 for noncoding genes).
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