proposeInteractions: Propose possible regulator-regulator interactions that could...

In birte: Bayesian Inference of Regulatory Influence on Expression (biRte)

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

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

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

birte documentation built on May 2, 2019, 12:32 a.m.