simulateData {birte} | R Documentation

## Simulate expression data.

### 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

    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

    data(humanNetworkSimul)
    sim = simulateData(affinities2)

[Package birte version 1.16.0 Index]