sismonr (version 2.1.0)

addEdge: Adds an edge in the in silico system's regulatory network.

Description

Adds an edge in the in silico system's regulatory network between specified genes.

Usage

addEdge(insilicosystem, regID, tarID, regsign = NULL, kinetics = list())

Arguments

insilicosystem

The in silico system (see createInSilicoSystem).

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 TC.pos.p, TL.pos.p or PTM.pos.p (depending on the type of regulation - regulation of RNA or protein decay can only be negative) provided in sysargs (see insilicosystemargs).

kinetics

Optional: named list of kinetics parameters of the reaction. If none provided, will be randomly chosen according to the parameters [name of the param]_samplingfct provided in sysargs (see insilicosystemargs). The parameters to provide depend on the type of regulation (i.e. parameter TargetReaction of the regulator):

• TargetReaction = "TC": the parameters to specify are "TCbindingrate", "TCunbindingrate" and "TCfoldchange";

• TargetReaction = "TL": the parameters to specify are "TLbindingrate", "TLunbindingrate" and "TLfoldchange";

• TargetReaction = "RD": the parameter to specify is "RDregrate";

• TargetReaction = "PD": the parameter to specify is "PDregrate";

• TargetReaction = "PTM": the parameter to specify is "PTMregrate".

Value

The modified in silico system.

Details

It must be noted that the type of regulation depends on the biological function of the regulator gene/complex (parameter TargetReaction).

Examples

# 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
# }