Simulate expression data.

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Description

The function draws expression data from a multivariate normal distribution with block structured co-variance matrix. First, data is drawn for a control condition (no active regulators). Then data is generated for the situation that a certain fraction of regulators is turned 'on' (treatment condition). Regulator activity states are sampled from a Bernoulli distribution.

Usage

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simulateData(affinities, nrep = 5, miRNAExpressions = TRUE, fn.targets = 0.1, 
fp.targets = 0.2, exp.nTF = 5, exp.nmiR = 5, exp.interact = 5)

Arguments

affinities

regulator-target gene network (see humanNetworkSimul)

nrep

number of replicates per condition

miRNAExpressions

Should miRNA expression data be simulated?

fn.targets

fraction of false negative target predictions (i.e. missing edges per regulator in the bipartite regulator-gene graph)

fp.targets

fraction of false positive target predictions

exp.nTF

expected number of active TFs

exp.nmiR

expected number of active miRNAs

exp.interact

expected number of active interaction terms

Details

If active interaction terms should be simulated, a set of possible interaction terms has to be defined in affinities$other.

Value

dat.mRNA

mRNA data – active regulators are expected to induce a log FC of 1

dat.miRNA

miRNA data – active miRNAs are expected to show a log FC of 1

dat.TF

TF expression data – active miRNAs are expected to show a log FC of 0.5

miRNAstates

simulated miRNA activities in treatment condition

TFstates

simulated TF activities in treatment condition

inter.states

simulated regulator interaction activities in treatment condition

Author(s)

Holger Froehlich

Examples

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