View source: R/in_silico_system.R
addEdge | R Documentation |
Adds an edge in the in silico system's regulatory network between specified genes.
addEdge(insilicosystem, regID, tarID, regsign = NULL, kinetics = list())
insilicosystem |
The in silico system (see |
regID |
Character. The ID of the regulator gene or complex. |
tarID |
Character. The ID of the target gene. |
regsign |
The sign of the regulation: either "1" (positive regulation) or "-1" (negative regulation). If none provided,
will be randomly chosen according to the parameter |
kinetics |
Optional: named list of kinetics parameters of the reaction. If none provided,
will be randomly chosen according to the parameters
|
It must be noted that the type of regulation depends on the biological function of the regulator gene/complex
(parameter TargetReaction
).
The modified in silico system.
## Not run: ## creates a system with no regulation mysystem = createInSilicoSystem(G = 10, PC.p = 1, PC.TC.p = 1, empty = TRUE) mysystem$edg mysystem2 = addEdge(mysystem, 1, 2, regsign = "1", kinetics = c("TCbindingrate"= 0.01, "TCunbindingrate" = 0.1, "TCfoldchange" = 10)) ## check all existing interactions in the system (no kinetic parameters) mysystem2$edg ## check the interactions targeting transcription, with kinetic parameters mysystem2$mosystem$TCRN_edg ## creates a system with no regulation mysystem = createInSilicoSystem(G = 5, PC.p = 1, PC.PD.p = 1, empty = TRUE) mysystem$edg mysystem2 = addEdge(mysystem, 1, 2) ## check all existing interactions in the system (no kinetic parameters) mysystem2$edg ## check the interactions targeting protein decay, with kinetic parameters mysystem2$mosystem$PDRN_edg ## End(Not run)
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