@@ -1,7 +1,7 @@

 Package: chromstaR

 Type: Package

 Title: Analysis of ChIP-Seq data for single and multiple histone modifications

-Version: 0.9.3

+Version: 0.9.4

 Date: 2014-05-03

 Author: Aaron Taudt, Maria Colome Tatche, Matthias Heinig, Minh Anh Nguyen

 Maintainer: Aaron Taudt <a.s.taudt@umcg.nl>

@@ -44,6 +44,11 @@

 #' @export

 callPeaksUnivariate2 <- function(binned.data, ID, prefit.on.chr, short=TRUE, eps=0.01, init="standard", max.time=NULL, max.iter=NULL, num.trials=1, eps.try=NULL, num.threads=1, read.cutoff=TRUE, read.cutoff.quantile=1, read.cutoff.absolute=500, max.mean=Inf, FDR=0.5, control=FALSE, keep.posteriors=FALSE, keep.densities=FALSE, verbosity=1) {

+	if (class(binned.data) == 'character') { 

+		message("Loading file ",binned.data)

+		binned.data <- get(load(binned.data))

+	}

+

 	pre.binned.data <- binned.data[seqnames(binned.data)==prefit.on.chr]

 	pre.model <- callPeaksUnivariate(pre.binned.data, ID=ID, eps=eps, init=init, max.time=max.time, max.iter=max.iter, num.trials=num.trials, eps.try=eps.try, num.threads=num.threads, read.cutoff=read.cutoff, read.cutoff.quantile=read.cutoff.quantile, read.cutoff.absolute=read.cutoff.absolute, max.mean=max.mean, FDR=FDR, control=control, keep.posteriors=FALSE, keep.densities=FALSE, verbosity=verbosity)

@@ -116,7 +116,7 @@ void R_univariate_hmm(int* O, int* T, int* N, double* size, double* prob, int* m

 				else if (i_state == 2)

 				{

 					//FILE_LOG(logDEBUG) << "Initializing size and prob for state 2";

-					imean = mean+1;

+					imean = mean*2;

 					ivariance = variance*2;

 				} 

 				// Make sure variance is greater than mean