getOmicsModules {SmCCNet}

Extract Omics Modules based on Similarity Matrix.

Description

Apply hierarchical tree cutting to the similarity matrix and extract multi/single-omics network modules.

Usage

getOmicsModules(Abar, CutHeight = 1 - 0.1^10, PlotTree = TRUE)

Arguments

Abar

A similary matrix for all features (all omics data types).

CutHeight

Height threshold for the hierarchical tree cutting. Default is 1-0.1^{10}.

PlotTree

Logical. Whether to create a hierarchical tree plot, default is set to TRUE.

Value

A list of multi/single-omics modules.

Examples

set.seed(123)
w <- rnorm(5)
w <- w/sqrt(sum(w^2))
feature_name <- paste0('feature_', 1:5)
abar <- getAbar(w, FeatureLabel = feature_name)
modules <- getOmicsModules(abar, CutHeight = 0.5)