# 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

1 | ```
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

1 2 3 | ```
# artificial data
data(humanNetworkSimul)
affinities2 = simplify(affinities2)
``` |