Add_DepthMatrix no longer works

[mfansler]

After updating to the latest version from v1.0.0, I can no longer get the Add_DepthMatrix to work on code that previously ran fine. I think there are actually a couple issues here:

redeemR/R/BuidTree.R

Lines 531 to 537 in c9de785

	definition=function(object,QualifiedTotalCts=""){
	require(reshape2)
	message("Remember to update for combined object")
	if(length(QualifiedTotalCts)==0){
	QualifiedTotalCts<-read.table(paste(object@attr$path,"/QualifiedTotalCts",sep=""))
	}
	colnames(QualifiedTotalCts)<-c("Cell","Pos","T","LS","S","VS")

First, it now needs the argument to be provided, which wasn't previously the case:

Error in Add_DepthMatrix(.) : 
  argument "QualifiedTotalCts" is missing, with no default

The apparent default argument in the signature is to pass "", but then it tests for length(QualifiedTotalCts) == 0, which is not true, which leads to erroring out on the colnames assignment:

Error in `colnames<-`(`*tmp*`, value = c("Cell", "Pos", "T", "LS", "S",  : 
  attempt to set 'colnames' on an object with less than two dimensions

I think the only actual argument that makes it work - outside manually loading the table - is QualifiedTotalCts=NULL. That is rather counterintuitive.