Propose possible regulator-regulator interactions that could be worthwhile to be tested into the biRte model.

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Description

The purpose is to identify interesting interactions terms for our model. Assuming the design matrix to be binary, the interaction term between two variables X1 and X2 is 1, if X1=1 AND X2=1 (zero, otherwise). The function computes the relative overlap between all pairs of variables X1 and X2 via the Tanimoto-Jaccard index. Variable pairs with cutoff.lower < Tanimoto-Jaccard < cutoff.upper are considered interesting candidates.

Usage

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proposeInteractions(affinities, cutoff.lower=0.1, cutoff.upper=0.8)

Arguments

affinities

original regulator-target gene network

cutoff.lower

lower range for Tanimoto-Jaccard index

cutoff.upper

upper range for Tanimoto-Jaccard index

Value

A list of the same format as affinities$TF and affinites$miRNA: Each list entry corresponds to the intersection of two target gene sets.

Author(s)

Holger Froehlich

Examples

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# artificial data
data(humanNetworkSimul)
affinities.int = proposeInteractions(affinities2)