estimateNetwork {birte} | R Documentation

## Estimate network between active regulators using Nested Effects Models (NEMs).

### Description

Given a biRte model, this function makes posterior inference about possible upstream-downstream relationships between active regulators. This is done based on observed differential expression of putative target genes. The idea is that regulator A acts upstream of regulator B, if differentially expressed targets of B are a subset of those of A.

### Usage

    estimateNetwork(model, thresh=0.1, select=c("marginal", "MAP"), method="pairwise",
    de.genes, bootstrap=0, typeII=0.1)

### Arguments

`model` | biRte model
`thresh` | cutoff for marginal posterior probabilities
`select` | "marginal": select regulators based on marginal posterior probabilities; "MAP": select regulators based on MAP configuration
`method` | algorithm used for NEM based network inference, see `nem`
`de.genes` | set of differentially expressed genes
`bootstrap` | optional: number of bootstrap replicates to draw (non-parameteric bootstrap)
`typeII` | assumed type-II error rate

### Value

nem-model

### Author(s)

Holger Froehlich

### Examples

    # see vignette

[Package birte version 1.16.0 Index]