simplify {birte} | R Documentation

## Simplify regulator-target gene network via clustering.

### Description

Several regulators (specifically TFs) might have extremely overlapping target genes. In order to identify clusters of highly similar regulators (mainly TFs) we implemented a network simplification algorithm in biRte: We construct the biadjacency matrix of the complete bipartite regulator target-gene graph and then calculate a single linkage clustering of regulators based on the Tanimoto-Jaccard similarity of their target genes. The dendrogram is cut at a defined height (default: 0.1) to idenfity resulting groups. The algorithm is meant to simplify the inference of active regulators, because the resulting regulator clusters have more dissimilar target gene profiles.

### Usage

    simplify(affinities, cutoff=0.9)

### Arguments

`affinities` | original regulator-target gene network
`cutoff` | cut dendrogram at height 1 - cutoff (i.e. similarity cutoff)

### Value

clustered / simplified network

### Author(s)

Holger Froehlich

### Examples

    # artificial data
    data(humanNetworkSimul)
    affinities2 = simplify(affinities2)

[Package birte version 1.20.0 Index]