sim.intervention: Simulate interventions in a Nested Effects Model

In cbg-ethz/pcNEM: Probabilistic combinatorial 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.

Author(s)

Holger Froehlich

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

cbg-ethz/pcNEM documentation built on Sept. 27, 2019, 8:58 a.m.