Prunes Subnetwork and Return Final Pruned Subnetwork Module

Prunes subnetworks with network pruning algorithm (see multi-omics vignette for detail), and save the final pruned subnetwork to the user-defined directory. The final subnetwork is an .Rdata file with a name 'size_m_net_ind.Rdata', where \(m\) is the final pruned network size, and ind is the index of the subnetwork module after hierarchical clustering.

Usage

networkPruning(
  Abar,
  CorrMatrix,
  data,
  Pheno,
  type,
  ModuleIdx,
  min_mod_size = 10,
  max_mod_size,
  damping = 0.9,
  method = "NetSHy",
  saving_dir
)

Arguments

Abar: Adjacency matrix of subnetwork with size \(m^{*}\) by \(m^{*}\) after hierarchical clustering.
CorrMatrix: The correlation matrix of features in Abar, it should be \(m^{*}\) by \(m^{*}\) as well.
data: The omics data for the subnetwork.
Pheno: The trait (phenotype) data used for network pruning.
type: A vector with length equal to total number of features in the adjacency matrix indicating the type of data for each feature. For instance, for a subnetwork with 2 genes and a protein, the type argument should be set to c('gene', 'gene', 'protein'), see multi-omics vignette for more information.
ModuleIdx: The index of the network module that summarization score is intended to be stored, this is used for naming the subnetwork file in user-defined directory.
min_mod_size: The minimally possible subnetwork size for the pruned network module, should be an integer from 1 to the largest possible size of the subnetwork, default is set to 10.
max_mod_size: the maximally possible subnetwork size for the pruned network module, should be an integer from 1 to the largest possible size of the subnetwork, and it needs to be greater than the value specified in min_mod_size.
damping: damping parameter for the PageRank algorithm, default is set to 0.9, see igraph package for more detail.
method: Selection between NetSHy' and 'PCA', specifying the network summarization method used for network pruning, default is set to NetSHy.
saving_dir: User-defined directory to store pruned subnetwork.

Value

A file stored in the user-defined directory, which contains the following: (1) correlation_sub: correlation matrix for the subnetwork. (2) M: adjacency matrix for the subnetwork. (3) omics_corelation_data: individual molecular feature correlation with phenotype. (4) pc_correlation: first 3 PCs correlation with phenotype. (5) pc_loading: principal component loadings. (6) pca_x1_score: principal component score and phenotype data. (7) mod_size: number of molecular features in the subnetwork. (8) sub_type: type of feature for each molecular features.

Examples

library(SmCCNet)
set.seed(123)
w <- rnorm(20)
w <- w/sqrt(sum(w^2))
labels <- paste0('feature_', 1:20)
abar <- getAbar(w, FeatureLabel = labels)
modules <- getOmicsModules(abar, CutHeight = 0.1)

x <- X1[ ,seq_len(20)]
corr <- stats::cor(x)
# display only example
# networkPruning(abar, corr, data = x, Pheno = Y,
# ModuleIdx = 1,  min_mod_size = 3, max_mod_size = 10, method = 'NetSHy', saving_dir = 
# )