@@ -1,5 +1,5 @@

 Package: bsseq

-Version: 0.9.0

+Version: 0.9.1

 Title: Analyze, manage and store bisulfite sequencing data

 Description: Tools for analyzing and visualizing bisulfite sequencing data

 Author: Kasper Daniel Hansen

@@ -237,9 +237,14 @@ print.summary.BSseqTstat <- function(x, ...) {

 plot.BSseqTstat <- function(x, y, ...) {

     tstat <- getStats(x)[, "tstat"]

-    tstat.cor <- getStats(x)[, "tstat.corrected"]

     plot(density(tstat), xlim = c(-10,10), col = "blue", main = "")

-    lines(density(tstat.cor), col = "black")

-    legend("topleft", legend = c("uncorrected", "corrected"), lty = c(1,1),

-           col = c("blue", "black"))

+    if("tstat.corrected" %in% colnames(getStats(x))) {

+        tstat.cor <- getStats(x)[, "tstat.corrected"]

+        lines(density(tstat.cor), col = "black")

+        legend("topleft", legend = c("uncorrected", "corrected"), lty = c(1,1),

+               col = c("blue", "black"))

+    } else {

+        legend("topleft", legend = c("uncorrected"), lty = 1,

+               col = c("blue"))

+    }

 }

@@ -23,22 +23,25 @@ dmrFinder <- function(BSseqTstat, cutoff = NULL, qcutoff = c(0.025, 0.975),

     regions

 }

-clusterMaker <- function(chr,pos,order.it=TRUE,maxGap=300){

-  nonaIndex=which(!is.na(chr) & !is.na(pos))

-  Indexes=split(nonaIndex,chr[nonaIndex])

-  clusterIDs=rep(NA,length(chr))

-  LAST=0

-  for(i in seq(along=Indexes)){

-    Index=Indexes[[i]]

-    x=pos[Index]

-    if(order.it){ Index=Index[order(x)];x=pos[Index] }

-    y=as.numeric(diff(x)>maxGap)

-    z=cumsum(c(1,y))

-    clusterIDs[Index]=z+LAST

-    LAST=max(z)+LAST

-  }

-  clusterIDs

-}  

+clusterMaker <- function(chr, pos, order.it=TRUE, maxGap=300){

+    nonaIndex <- which(!is.na(chr) & !is.na(pos))

+    Indexes <- split(nonaIndex, chr[nonaIndex])

+    clusterIDs <- rep(NA, length(chr))

+    LAST <- 0

+    for(i in seq(along = Indexes)){

+        Index <- Indexes[[i]]

+        x <- pos[Index]

+        if(order.it){

+            Index <- Index[order(x)]

+            x <- pos[Index]

+        }

+        y <- as.numeric(diff(x) > maxGap)

+        z <- cumsum(c(1, y))

+        clusterIDs[Index] <- z + LAST

+        LAST <- max(z) + LAST

+    }

+    clusterIDs

+}

 regionFinder3 <- function(x, chr, positions, keep, maxGap = 300, verbose = TRUE) {

@@ -13,10 +13,10 @@ plotAnnoTrack <- function(gr, annoTrack) {

         })

 }

-plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addRegions = NULL, annoTrack = NULL, 

-                            col = NULL, lty = NULL, lwd = NULL, BSseqTstat = NULL, mainWithWidth = TRUE,

-                            regionCol = alpha("red", 0.1), addTicks = TRUE, addPoints = FALSE,

-                            pointsMinCov = 5, highlightMain = FALSE, verbose = TRUE) {

+plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addRegions = NULL,

+                            annoTrack = NULL, col = NULL, lty = NULL, lwd = NULL, BSseqTstat = NULL,

+                            mainWithWidth = TRUE, regionCol = alpha("red", 0.1), addTicks = TRUE,

+                            addPoints = FALSE, pointsMinCov = 5, highlightMain = FALSE, verbose = TRUE) {

     cat("preprocessing ...")

     if(!is.null(regions)) {

         if(is(regions, "data.frame"))

@@ -69,6 +69,7 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg

     ## regions <- pintersect(region, rep(gr, length(regions)))

     ## regions <- regions[width(regions) == 0]

     regions <- subsetByOverlaps(regions, gr)

+    regions <- pintersect(regions, rep(gr, length(regions)))

     if(length(regions) == 0)

         return(NULL)

     rect(xleft = start(regions), xright = end(regions), ybottom = ylim[1],

@@ -115,7 +116,7 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg

                            format(plotRange[2], big.mark = ",", scientific = FALSE))

     if(mainWithWidth) {

         regionWidth <- sprintf("width = %s, extended = %s", 

-                               format(width(gr) - 2*extend, big.mark = ",", scientific = FALSE),

+                               format(width(gr), big.mark = ",", scientific = FALSE),

                                format(extend, big.mark = ",", scientific = FALSE))

         regionCoord <- sprintf("%s (%s)", regionCoord, regionWidth)

     }

@@ -2,6 +2,14 @@

 \title{bsseq news}

 \encoding{UTF-8}

+\section{Version 0.7.x}{

+  \itemize{

+    \item Fixed a problem with "width" in the title of bsseq plots.

+    \item plot.BSseqTstat now allows for BSseqTstat objects computed

+    without correction.

+  }

+}

+

 \section{Version 0.7.x}{

   \itemize{

     \item Removed the returnRaw argument to read.bismark() as it was