SmCCNet (version 2.0.3)

networkPruning: Prunes Subnetwork and Return Final Pruned Subnetwork Module

Description

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
)

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.

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.

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 = 
# )