R/esetMicroRna.R

In AgiMicroRna: Processing and Differential Expression Analysis of Agilent microRNA chips

`esetMicroRna` <-
function(uRNAList,targets,makePLOT=FALSE,verbose=FALSE) {

	
	if (!is(uRNAList, "uRNAList")){
	  stop("'input' must be a uRNAList",call. = FALSE)
   	 	if (is.null(dim(uRNAList)[1])) {
        		stop("'input' is empty",call. = FALSE)
	 	}
	}

	if(missing(targets)){
		stop("'targets' is missing ",call. = FALSE)
	}

	if("GErep" %in% colnames(targets)){
		GErep=targets$GErep 
		nGE=sum(table(table(GErep)))
		g1=targets$GErep  # g1 must be numeric, from 1:n
		g2=rownames(targets)
	}else{
		stop("'targets' needs 'GErep' field")
	}

	goON=all(rownames(targets) == colnames(uRNAList$iTGS))
		if(!goON){
		stop("rownames in pData(targets) different from colnames uRNAList$TGS",call. = FALSE)
		}
		phenoData=new("AnnotatedDataFrame",data=targets)

	TMP=uRNAList$TGS
	rownames(TMP)=uRNAList$genes$GeneName
	colnames(TMP)=g2
	nGEN=dim(TMP)[1]
	nARR=dim(TMP)[2]

	esetPROC = new("ExpressionSet", exprs = TMP, phenoData = phenoData)
	
	if(verbose){
	cat("outPUT DATA: esetPROC","\n")
	print(dim(esetPROC))
	cat("------------------------------------------------------","\n")
	}

	if(!missing(makePLOT)){
	if(makePLOT){

	dev.new()
	hierclusMicroRna(exprs(esetPROC),GErep,methdis="euclidean",
        methclu="complete",sel=FALSE,100)

	dev.new()
	size=100

	maintitle="50 High Variance"
	HeatMapMicroRna(exprs(esetPROC),50,maintitle)

	dev.new()
	PCAplotMicroRna(esetPROC,targets)
	}
	}

return(esetPROC)

} # end function