cytOutData-methods {categoryCompare} | R Documentation |
cytOutData
Takes the saveObj
generated by cytOutNodes
and writes the data to a file
A text file with the annotations previously saved using cytOutNodes
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")
## 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)