breakEdges-methods: Methods for Function 'breakEdges' in Package...

In categoryCompare: Meta-analysis of high-throughput experiments using feature annotations

Description

Methods for function breakEdges in package categoryCompare

Methods

signature(cwObject = "ccCompareResult", cutoff = "numeric")

Allows one to remove edges in the ccCompareResult mainGraph slot prior to passing it into Cytoscape for visualization. Given that the number of edges can be rather large (especially for Gene Ontology) this can easily speed up the transfer, without actually losing any information.

signature(cwObject = "numeric", cutoff = "numeric")

Once an annotation graph is in Cytoscape, remove edges above or below the cutoff. Note that this does not affect the original graph in the ccCompareResult object.

Author(s)

Robert M Flight

See Also

breakEdges ccCompareResult ccOutCyt

Examples

data(ccData)

# breaking the edges in a ccCompareResult
ccResults$BP <- breakEdges(ccResults$BP, 0.8)
## Not run: 
hasCy <- (if (.Platform$OS.type %in% "windows") {
(length(grep("Cytoscape", system("tasklist", intern=TRUE))) > 0)})

if hasCy {

	cwObj <- ccOutCyt(ccResults$BP,ccOpts)
	# now breaking them in the CytoscapeWindow object
	breakEdges(cwObj, 0.85)
	Sys.sleep(10)
	RCy3::deleteWindow(cwObj)
	}

## End(Not run)

categoryCompare documentation built on Nov. 8, 2020, 5:59 p.m.