R/funcClustAnnot.R

In uc-bd2k/CLEAN: Clustering Enrichment Analysis

`funcClustAnnot` <-
function(data = NULL, 
		rclust = NULL, 
		cclust = NULL, 
		funcCategories = NULL, 
		fClustAnnotations = NULL,
		bkgList = NULL,
		file = "cluster", 
		maxSize=1000, 
		minSize=10, 
		minGenesInCategory=10,
		maxGenesInCategory=1000,
		minSigsInCategory=2,
		inBkg=TRUE,
		sigFDR = 0.1,
		addCLEANscore2cdt = TRUE,
		species = NULL,
		estimateNullDistribution = FALSE,
		atr.distance="euc",
		gtr.distance="euc",
		dec='.',
		digits=5,
		verbose=TRUE, 
		saveDataObjects = FALSE,
		sampleDesc = NULL,
		callTreeView = FALSE) {
	warning("funcClustAnnot() is deprecated.  Please use generateTreeViewFiles() or runCLEAN() instead")
	generateTreeViewFiles(data = data, rclust = rclust, cclust = cclust, functionalCategories = funcCategories,
		fClustAnnotations = fClustAnnotations, bkgList = bkgList, file = file, maxSize = maxSize, minSize=minSize,
		minGenesInCategory = minGenesInCategory, maxGenesInCategory = maxGenesInCategory, 
		inBkg = inBkg, sigFDR = sigFDR, addCLEANscore2cdt = addCLEANscore2cdt,
		species = species, estimateNullDistribution = estimateNullDistribution, dec=dec, 
		verbose = verbose, saveDataObjects = saveDataObjects,
		sampleDesc = sampleDesc, callTreeView = callTreeView)
}