exportNetworkToCytoscape: Export network to Cytoscape

In WGCNA: Weighted Correlation Network Analysis

Export network to Cytoscape

Description

This function exports a network in edge and node list files in a format suitable for importing to Cytoscape.

Usage

exportNetworkToCytoscape(
   adjMat,
   edgeFile = NULL,
   nodeFile = NULL,
   weighted = TRUE,
   threshold = 0.5,
   nodeNames = NULL,
   altNodeNames = NULL,
   nodeAttr = NULL,
   includeColNames = TRUE)

Arguments

adjMat	adjacency matrix giving connection strengths among the nodes in the network.
edgeFile	file name of the file to contain the edge information.
nodeFile	file name of the file to contain the node information.
weighted	logical: should the exported network be weighted?
threshold	adjacency threshold for including edges in the output.
nodeNames	names of the nodes. If not given, dimnames of adjMat will be used.
altNodeNames	optional alternate names for the nodes, for example gene names if nodes are labeled by probe IDs.
nodeAttr	optional node attribute, for example module color. Can be a vector or a data frame.
includeColNames	logical: should column names be included in the output files? Note that Cytoscape can read files both with and without column names.

Details

If the corresponding file names are supplied, the edge and node data is written to the appropriate files. The edge and node data is also returned as return value (see below).

Value

A list with the following componens:

egdeData	a data frame containing the edge data, with one row per edge
nodeData	a data frame containing the node data, with one row per node

Author(s)

Peter Langfelder

See Also

exportNetworkToVisANT

WGCNA documentation built on Sept. 18, 2024, 5:08 p.m.