summarizeNetSHy {SmCCNet}

NetSHy Summarization Score

Description

Implement NetSHy network summarization via a hybrid approach (Vu et al.,) to summarize network by considering the network topology with Laplacian matrix.

Usage

summarizeNetSHy(X, A, npc = 1)

Arguments

X

An n\times m data matrix with m features and n subjects.

A

Corresponding adjacency matrix of size p by p.

npc

Number of principal components used to summarize the network, default is set to 1.

Value

A list consists of (1) subject-level network summarization score, (2) principal component importance information: standard deviation, percent of variance explained, and cumulative proportion of variance explained, and (3) principal component feature-level loadings.

References

Vu, Thao, Elizabeth M. Litkowski, Weixuan Liu, Katherine A. Pratte, Leslie Lange, Russell P. Bowler, Farnoush Banaei-Kashani, and Katerina J. Kechris. "NetSHy: network summarization via a hybrid approach leveraging topological properties." Bioinformatics 39, no. 1 (2023): btac818.

Examples

# simulate omics data
OmicsData <- matrix(rnorm(200,0,1), nrow = 10, ncol = 20)
# simulate omics adjacency matrix
set.seed(123)
w <- rnorm(20)
w <- w/sqrt(sum(w^2))
featurelabel <- paste0('omics',1:20)
abar <- getAbar(w, FeatureLabel = featurelabel)
# extract NetSHy summarization score
netshy_score <- summarizeNetSHy(OmicsData, abar)