wto {EGAnet}

Weighted Topological Overlap

Description

Computes weighted topological overlap following the Novick et al. (2009) definition

Usage

wto(network, signed = TRUE, diagonal.zero = TRUE)

Arguments

network

Symmetric matrix or data frame. A symmetric network

signed

Boolean (length = 1). Whether the signed version should be used. Defaults to TRUE. Use FALSE for absolute values

diagonal.zero

Boolean (length = 1). Whether diagonal of overlap matrix should be set to zero. Defaults to TRUE. Use FALSE to allow overlap of a node with itself

Value

A symmetric matrix of weighted topological overlap values between each pair of variables

References

Original formalization
Nowick, K., Gernat, T., Almaas, E., & Stubbs, L. (2009). Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain. Proceedings of the National Academy of Sciences, 106, 22358-22363.

Examples

# Obtain network
network <- network.estimation(wmt2[,7:24], model = "glasso")

# Compute wTO
wto(network)