nem (version 2.46.0)

sim.intervention: Simulate interventions in a Nested Effects Model

Description

Simulates a knock-down of a list of network nodes and returns the network nodes and effect reporters, where effects are expected.

Usage

sim.intervention(x, int, T=1)

Arguments

x

nem object

int

a character vector of nodes in the network

T

number of time steps to be simulated (only for dynoNEMs)

Value

list with two slots:

Sgenes.effected

effected network nodes (by intervention)

Egenes.effected

most likely effected downstream effect reporters (by intervention)

Egenes.effected.prob

probability of each reporter to be effected by the respective intervention experiment.

Examples

   data("BoutrosRNAi2002")
   D <- BoutrosRNAiDiscrete[,9:16]
   res = nem(D, control=set.default.parameters(unique(colnames(D)), para=c(0.13,0.05))) 
   sim.intervention(res, "rel") # simulate knock-down of rel