cytOutData-methods: Methods for Function 'cytOutData'

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

Methods for Function cytOutData

Description

Takes the saveObj generated by cytOutNodes and writes the data to a file

Value

A text file with the annotations previously saved using cytOutNodes

Methods

signature(saveObj = "list", compareResult = "ccCompareResult", mergedData = "mergedData")

saveObj is the list object generated by cytOutNodes, compareResult is the object from ccCompare, and mergedData is created using mergeLists, but is optional.

...

: optional arguments also include: orgType, default is "header" where each group is seperate, "annotate" pushes all the data into one table with a new column that designates which groups the annotation was found in; fileName, the name of a text file to output the results to; displayFile, whether or not to display the file (default is "FALSE")

Examples

## Not run: 
hasCy <- (if (.Platform$OS.type %in% "windows") {
(length(grep("Cytoscape", system("tasklist", intern=TRUE))) > 0)})

if hasCy {
	data(ccData)
	ccResults$BP <- breakEdges(ccResults$BP, 0.8)
	cwObj <- ccOutCyt(ccResults$BP,ccOpts)
	# user selects some nodes in Cytoscape
	RCy3::selectNodes(cwObj, c("GO:0007017", "GO:0000226", "GO:0007051", "GO:0007052"))
	savedNodes <- cytOutNodes("random1", cwObj) # save them
	# and selects some other nodes
	RCy3::selectNodes(cwObj,
	c("GO:0071103", "GO:0034728", "GO:0006323", "GO:0030261", "GO:0006334"),
	preserve.current.selection=FALSE)
	savedNodes <- cytOutNodes("random2", cwObj, savedNodes)

	# now spit results out to a file
	cytOutData(savedNodes, ccResults$BP)
}
## End(Not run)

rmflight/categoryCompare documentation built on April 25, 2024, 11:20 a.m.