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

 Package: bsseq

-Version: 0.11.2

+Version: 0.11.3

 Title: Analyze, manage and store bisulfite sequencing data

 Description: Tools for analyzing and visualizing bisulfite sequencing data

 Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),

@@ -88,8 +88,8 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg

         else

             col <- rep("black", nrow(pData(object)))

     }

-    if(length(col) != nrow(object))

-        col <- rep(col, length.out = nrow(object))

+    if(length(col) != ncol(object))

+        col <- rep(col, length.out = ncol(object))

     if(is.null(names(col)))

         names(col) <- sampleNames(object)

@@ -97,10 +97,10 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg

         if("lty" %in% names(pData(object)))

             lty <- pData(object)[["lty"]]

         else

-            lty <- rep(1, nrow(pData(object)))

+            lty <- rep(1, ncol(object))

     }

-    if(length(lty) != nrow(object))

-        lty <- rep(lty, length.out = nrow(object))

+    if(length(lty) != ncol(object))

+        lty <- rep(lty, length.out = ncol(object))

     if(is.null(names(lty)))

         names(lty) <- sampleNames(object)

@@ -110,8 +110,8 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg

         else

             lwd <- rep(1, nrow(pData(object)))

     }

-    if(length(lty) != nrow(object))

-        lty <- rep(lty, length.out = nrow(object))

+    if(length(lty) != ncol(object))

+        lty <- rep(lty, length.out = ncol(object))

     if(is.null(names(lwd)))

         names(lwd) <- sampleNames(object)

@@ -7,7 +7,10 @@

     \item Converted to using Authors@R in the DESCRIPTIOn file.

     \item plotRegion did not respect the col/lty/lwd argument if given

     explicitely as opposed to through pData().  Reported by Karen

-    Conneely <kconnee@emory.edu>. 

+    Conneely <kconnee@emory.edu>.

+    \item Fixed an issue introduced by the previous change (to

+    plotRegion).  Reported (with a fix) by Tim Triche Jr

+    <tim.triche@gmail.com>.

   }

 }

@@ -4,6 +4,7 @@

 \alias{BSseqTstat}

 \alias{BSseqTstat-class}

 \alias{[,BSseqTstat-method}

+\alias{[,BSseqTstat,ANY-method}

 \alias{show,BSseqTstat-method}

 \title{Class BSseqTstat}

 \description{

@@ -3,6 +3,7 @@

 \docType{class}

 \alias{hasGRanges-class}

 \alias{[,hasGRanges-method}

+\alias{[,hasGRanges,ANY-method}

 \alias{end,hasGRanges-method}

 \alias{end<-,hasGRanges-method}

 \alias{granges,hasGRanges-method}