Description Usage Arguments Details Value Examples
View source: R/in_silico_system.R
Adds an edge in the in silico system's regulatory network between specified genes.
1 |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## 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
|
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