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

 Package: chromstaR

 Type: Package

 Title: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

-Version: 1.5.2

+Version: 1.5.3

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

 Maintainer: Aaron Taudt <aaron.taudt@gmail.com>

 Description: This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses.

@@ -1,3 +1,11 @@

+CHANGES IN VERSION 1.5.3

+------------------------

+

+SIGNIFICANT USER-LEVEL CHANGES

+

+    o Function 'changePostCutoff()' works on univariate peak calls without posterior needing to be present.

+    

+    

 CHANGES IN VERSION 1.5.1

 ------------------------

@@ -448,13 +448,20 @@ changePostCutoff.univariate <- function(model, post.cutoff) {

     threshold <- post.cutoff

     model$post.cutoff <- post.cutoff

-    if (is.null(model$bins$posteriors)) stop("Cannot recalculate states because posteriors are missing. Run 'callPeaksUnivariate' again with option 'keep.posteriors' set to TRUE.")

+    if (is.null(model$bins$posteriors) & is.null(model$bins$posterior.modified)) stop("Cannot recalculate states because posteriors are missing. Run 'callPeaksUnivariate' again with option 'keep.posteriors' set to TRUE.")

+    

     ## Calculate states

     ptm <- startTimedMessage("Calculating states from posteriors ...")

-    states <- rep(NA,length(model$bins))

-    states[ model$bins$posteriors[,3]<threshold & model$bins$posteriors[,2]<=model$bins$posteriors[,1] ] <- 1

-    states[ model$bins$posteriors[,3]<threshold & model$bins$posteriors[,2]>model$bins$posteriors[,1] ] <- 2

-    states[ model$bins$posteriors[,3]>=threshold ] <- 3

+    if (is.null(model$bins$posteriors)) {

+        warning("Using column 'posterior.modified' to recalculate states, there will be no state 'zero-inflation' in the output. Run 'callPeaksUnivariate' again with option 'keep.posteriors' set to TRUE to also obtain 'zero-inflation' states.")

+        states <- rep(2,length(model$bins))

+        states[ model$bins$posterior.modified>=threshold ] <- 3

+    } else {

+        states <- rep(NA,length(model$bins))

+        states[ model$bins$posteriors[,3]<threshold & model$bins$posteriors[,2]<=model$bins$posteriors[,1] ] <- 1

+        states[ model$bins$posteriors[,3]<threshold & model$bins$posteriors[,2]>model$bins$posteriors[,1] ] <- 2

+        states[ model$bins$posteriors[,3]>=threshold ] <- 3

+    }

     states <- state.labels[states]

     model$bins$state <- states

     stopTimedMessage(ptm)