getEdgeList: Converts an adjacency matrix into edge list representation

In PCIT: Partial Correlation Coefficient with Information Theory

Description

Given an adjacency matrix, converts it into edge list representation. This edge list can be written to a file for easy import into other software such as cytoscape.

Only the upper triangle is returned as it is assumed the matrix is symmetric. The edge list is returned as a data frame with 3 columns: 'From', 'To' and 'Weight'.

Usage

	getEdgeList(m, rm.zero=TRUE)

Arguments

m	- An adjacency matrix.
rm.zero	- A boolean to indicate whether zero weight edges should be excluded from the edge list.

Author(s)

Nathan S. Watson-Haigh

Examples

	data(PCIT)
	m <- m[1:200,1:200]        # just use a small subset of the data
	
	el <- getEdgeList(m)
	
	# modify the edge list to include some useful attributes for cytoscape
	el$sign[el$Weight<0] <- '-'
	el$sign[el$Weight>0] <- '+'
	el$Weight <- abs(el$Weight)
	# write the edge list stuff to a file suitable for import into cytoscape
	write.table(el, file="el.txt", row.names=FALSE, col.names=TRUE, sep="\t",
		quote=FALSE)

Example output

PCIT documentation built on May 1, 2019, 8:10 p.m.