wgcna2graphDF: Convert adjacency or TOM matrix to igraph data.frame

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Convert adjacency or TOM matrix to igraph data.frame

Description

Convert TOM matrix (from WGCNA analysis) to igraph data.frame and filter top connections. Uses igraph::graph_from_adjacency_matrix to convert matrix to data.frame.

Usage

wgcna2graphDF(
  w.mat,
  top.n = NULL,
  top.percentile = NULL,
  graph.type = "undirected"
)

Arguments

w.mat	TOM or adjacency matrix.
top.n	Numeric specifying N top connections to return (N < number of connections). If top.n and top.percentile are NULL, all connections retained.
top.percentile	Numeric [0,1] specifying Nth percetile of top connections to return. If top.n and top.percentile are NULL, all connections retained.
graph.type	Type of graph. Default is "undirected"

Value

igraph data.frame

Author(s)

Nicholas Mikolajewicz

Examples

# get connectivity for specified module
module.name <- names(module.list.all)[names(module.list.all) %in% which.modules]
module.gene.cur <- module.list.all[[module.name]]
w.cur <- w.mat[rownames(w.mat) %in% module.gene.cur, colnames(w.mat) %in% module.gene.cur]

# get igraph data.frame for subset of connections
w.df.top <- wgcna2graphDF(w.cur, top.n = top.n.interactions)
w.df.top$module.membership <- module.name

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.