Translate TOM matrin to create graph object

Translate TOM matrin to create graph object

Usage

trans_TOM_in_WGCNA(TOM, mat, threshold = NULL, top_k = NULL)

Arguments

TOM

matrix TOM matrix from WGCNA result

mat

matrix matrox to WGCNA analysis

threshold

numeric Absolute-weight cutoff. Edges with abs(weight) <= threshold are dropped. Set to NULL (default) to skip.

top_k

integer Per-node top-k nearest-neighbour sparsification. For each node, only its k strongest TOM neighbours are eligible to contribute edges. An undirected edge (i, j) survives if j is in i's top-k or i is in j's top-k (mutual-kNN union, the standard choice for WGCNA visualization). Set to NULL (default) to skip. Typical values for WGCNA plots are 10 - 30.

Value

A Data frame contain from, to and weight

Examples

if (FALSE) { # \dontrun{
# `TOM` is a topological overlap matrix from WGCNA and `mat` is the
# expression matrix used to compute it.

# Simple absolute-weight threshold:
edge_df <- trans_TOM_in_WGCNA(TOM = TOM, mat = mat, threshold = 0.1)

# Per-node top-20 neighbours (recommended for visualization):
edge_df <- trans_TOM_in_WGCNA(TOM = TOM, mat = mat, top_k = 20)

# Combine: top-20 per node, then drop anything below 0.05 globally.
edge_df <- trans_TOM_in_WGCNA(TOM = TOM, mat = mat,
                              threshold = 0.05, top_k = 20)
head(edge_df)
} # }