simplify: Simplify regulator-target gene network via clustering.

Description Usage Arguments Value Author(s) Examples

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


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