diff --git a/DESCRIPTION b/DESCRIPTION
index 97c27cf..c0102dd 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -56,7 +56,6 @@ Suggests:
     tidyverse
 Collate:
     utils.R
-    hasGRanges.R
     BSseq-class.R
     BSseqTstat_class.R
     MethylCounts.R
diff --git a/NAMESPACE b/NAMESPACE
index 1848f8b..04bd11c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -55,12 +55,10 @@ importFrom(R.utils, "isGzipped", "isBzipped", "gunzip", "bunzip2")
 ## Exporting
 ##
 
-exportClasses("hasGRanges",
-              "BSseq",
+exportClasses("BSseq",
               "BSseqTstat",
               "BSseqStat",
-              "MethylCounts",
-              "matrixOrNULL")
+              "MethylCounts")
 
 exportMethods("[", "show",
               "seqnames", "seqnames<-",
diff --git a/R/BSmooth.R b/R/BSmooth.R
index 79b4f9b..c1ae463 100644
--- a/R/BSmooth.R
+++ b/R/BSmooth.R
@@ -1,7 +1,7 @@
 # Internal functions -----------------------------------------------------------
 
-.rowTickmarks <- function(hasGRanges, maxGap) {
-    gr <- granges(hasGRanges)
+.rowTickmarks <- function(BSseq, maxGap) {
+    gr <- granges(BSseq)
     # NOTE: This relies on 'gr' being sorted, so really want to be sure of this!
     stopifnot(!is.unsorted(gr))
     clusters <- reduce(gr, min.gapwidth = maxGap, with.revmap = TRUE)
@@ -13,7 +13,7 @@
 makeClusters <- function(hasGRanges, maxGap = 10^8) {
     chrOrder <- as.character(runValue(seqnames(hasGRanges)))
     if(anyDuplicated(chrOrder))
-        stop("argument 'hasGRanges' is not properly order")
+        stop("argument 'hasGRanges' is not properly ordered")
     grBase <- granges(hasGRanges)
     clusters <- reduce(resize(grBase, width = 2*maxGap + 1, fix = "center"))
     start(clusters) <- pmax(rep(1, length(clusters)), start(clusters))
diff --git a/R/BSmooth.fstat.R b/R/BSmooth.fstat.R
index f1ec98f..f30e344 100644
--- a/R/BSmooth.fstat.R
+++ b/R/BSmooth.fstat.R
@@ -53,7 +53,7 @@ smoothSds <- function(BSseqStat, k = 101, qSd = 0.75, mc.cores = 1,
         stop("need to set argument 'maxGap'")
     if(verbose) cat("[smoothSds] preprocessing ... ")
     ptime1 <- proc.time()
-    clusterIdx <- makeClusters(granges(BSseqStat), maxGap = maxGap)
+    clusterIdx <- makeClusters(BSseqStat, maxGap = maxGap)
     ptime2 <- proc.time()
     stime <- (ptime2 - ptime1)[3]
     if(verbose) cat(sprintf("done in %.1f sec\n", stime))
@@ -137,7 +137,7 @@ localCorrectStat <- function(BSseqStat, threshold = c(-15,15), mc.cores = 1, ver
     maxGap <- BSseqStat$parameters$maxGap
     if(verbose) cat("[BSmooth.tstat] preprocessing ... ")
     ptime1 <- proc.time()
-    clusterIdx <- makeClusters(BSseqStat$gr, maxGap = maxGap)
+    clusterIdx <- makeClusters(BSseqStat, maxGap = maxGap)
     ptime2 <- proc.time()
     stime <- (ptime2 - ptime1)[3]
     if(verbose) cat(sprintf("done in %.1f sec\n", stime))
diff --git a/R/BSseqStat_class.R b/R/BSseqStat_class.R
index 4108622..9e0fd85 100644
--- a/R/BSseqStat_class.R
+++ b/R/BSseqStat_class.R
@@ -1,4 +1,4 @@
-setClass("BSseqStat", contains = "hasGRanges",
+setClass("BSseqStat", contains = "GRanges",
          representation(stats = "list",
                         parameters = "list")
          )
@@ -9,7 +9,7 @@ setValidity("BSseqStat", function(object) {
        anyDuplicated(names(object@stats)))
         msg <- validMsg(msg, "the 'stats' list needs to be named with unique names.")
     for(name in c("rawSds", "smoothsSds", "stat", "rawTstats")) {
-        if(name %in% names(object@stats) && isTRUE(nrow(object@stats[[name]]) != length(object@gr)))
+        if(name %in% names(object@stats) && isTRUE(nrow(object@stats[[name]]) != length(object)))
             msg <- validMsg(msg, sprintf("component '%s' of slot 'stats' has to have the same number of rows as slot 'gr' is long", name))
     }
     if(is.null(msg)) TRUE else msg
@@ -24,11 +24,7 @@ setMethod("show", signature(object = "BSseqStat"),
           })
 
 setMethod("[", "BSseqStat", function(x, i, ...) {
-    if(missing(i))
-        stop("need [i] for subsetting")
-    if(missing(i))
-        return(x)
-    x@gr <- x@gr[i]
+    i <- normalizeSingleBracketSubscript(i, x)
     statnames <- names(x@stats)
     names(statnames) <- statnames
     x@stats <- lapply(statnames, function(nam) {
@@ -38,17 +34,32 @@ setMethod("[", "BSseqStat", function(x, i, ...) {
         }
         x@stats[[nam]]
     })
-    x
+    callNextMethod()
 })
 
 BSseqStat <- function(gr = NULL, stats = NULL, parameters = NULL) {
-    out <- new("BSseqStat")
-    out@gr <- gr
-    out@stats <- stats
-    out@parameters <- parameters
-    out
+    new("BSseqStat", gr, stats = stats, parameters = parameters)
 }
 
+setMethod("updateObject", "BSseqStat",
+    function(object, ..., verbose = FALSE) {
+        if (!.hasSlot(object, "gr")) {
+            return(callNextMethod())
+        }
+        if (verbose)
+            message("[updateObject] ", class(object), " object ",
+                    "uses old internal representation from\n",
+                    "[updateObject] bsseq <= 1.49.2. ",
+                    "Updating it ... ", appendLF=FALSE)
+        gr <- updateObject(object@gr)
+        ans <- BSseqStat(gr = gr, stats = object@stats,
+                                  parameters = object@parameters)
+        if (verbose)
+            message("OK")
+        ans
+    }
+)
+
 # TODO: updateObject() to use ordinary matrix instead of DelayedMatrix with
 #       in-memory seed.
 # setMethod("updateObject", "BSseqStat",
diff --git a/R/BSseqTstat_class.R b/R/BSseqTstat_class.R
index a1dee49..cbcf7ad 100644
--- a/R/BSseqTstat_class.R
+++ b/R/BSseqTstat_class.R
@@ -1,11 +1,14 @@
-setClass("BSseqTstat", contains = "hasGRanges",
-         representation(stats = "matrix",
+## Add new union members as needed (e.g. "SparseMatrix").
+setClassUnion("matrix_OR_DelayedMatrix", c("matrix", "DelayedMatrix"))
+
+setClass("BSseqTstat", contains = "GRanges",
+         representation(stats = "matrix_OR_DelayedMatrix",
                         parameters = "list")
          )
 setValidity("BSseqTstat", function(object) {
     msg <- NULL
-    if(length(object@gr) != nrow(object@stats))
-        msg <- c(msg, "length of 'gr' is different from the number of rows of 'stats'")
+    if(length(object) != nrow(object@stats))
+        msg <- c(msg, "'stats' must have one row per methylation locus")
     if(is.null(msg)) TRUE else msg
 })
 
@@ -20,21 +23,13 @@ setMethod("show", signature(object = "BSseqTstat"),
           })
 
 setMethod("[", "BSseqTstat", function(x, i, ...) {
-    if(missing(i))
-        stop("need [i] for subsetting")
-    if(missing(i))
-        return(x)
-    x@gr <- x@gr[i]
+    i <- normalizeSingleBracketSubscript(i, x)
     x@stats <- x@stats[i,, drop = FALSE]
-    x
+    callNextMethod()
 })
 
 BSseqTstat <- function(gr = NULL, stats = NULL, parameters = NULL) {
-    out <- new("BSseqTstat")
-    out@gr <- gr
-    out@stats <- stats
-    out@parameters <- parameters
-    out
+    new("BSseqTstat", gr, stats = stats, parameters = parameters)
 }
 
 summary.BSseqTstat <- function(object, ...) {
@@ -68,10 +63,20 @@ plot.BSseqTstat <- function(x, y, ...) {
 }
 
 setMethod("updateObject", "BSseqTstat",
-          function(object, ...) {
-              stats <- object@stats
-              stats <- stats
-              object@stats <- stats
-              object
-          }
+    function(object, ..., verbose = FALSE) {
+        if (!.hasSlot(object, "gr")) {
+            return(callNextMethod())
+        }
+        if (verbose)
+            message("[updateObject] ", class(object), " object ",
+                    "uses old internal representation from\n",
+                    "[updateObject] bsseq <= 1.49.2. ",
+                    "Updating it ... ", appendLF=FALSE)
+        gr <- updateObject(object@gr)
+        ans <- BSseqTstat(gr = gr, stats = object@stats,
+                                   parameters = object@parameters)
+        if (verbose)
+            message("OK")
+        ans
+    }
 )
diff --git a/R/hasGRanges.R b/R/hasGRanges.R
deleted file mode 100644
index 8742879..0000000
--- a/R/hasGRanges.R
+++ /dev/null
@@ -1,135 +0,0 @@
-setClassUnion("matrixOrNULL", c("matrix", "NULL"))
-
-setClass("hasGRanges",
-         representation(gr = "GRanges"))
-
-setMethod("seqnames", signature(x = "hasGRanges"), function(x) {
-    seqnames(x@gr)
-})
-setReplaceMethod("seqnames", "hasGRanges", function(x, value) {
-    seqnames(x@gr) <- value
-    x
-})
-
-setMethod("seqlevels", signature(x = "hasGRanges"), function(x) {
-    seqlevels(x@gr)
-})
-setReplaceMethod("seqlevels", "hasGRanges", function(x, value) {
-    seqlevels(x@gr) <- value
-    x
-})
-
-setMethod("seqlengths", signature(x = "hasGRanges"), function(x) {
-    seqlengths(x@gr)
-})
-setReplaceMethod("seqlengths", "hasGRanges", function(x, value) {
-    seqlengths(x@gr) <- value
-    x
-})
-
-setMethod("granges", signature(x = "hasGRanges"),
-    function(x, use.names = TRUE, use.mcols = FALSE, ...)
-        granges(x@gr, use.names = use.names, use.mcols = use.mcols, ...)
-)
-
-## FIXME: might want a granges replacement function
-
-setMethod("start", "hasGRanges", function(x, ...) {
-    start(x@gr, ...)
-})
-setReplaceMethod("start", "hasGRanges", function(x, check = TRUE, value) {
-    start(x@gr, check = check) <- value
-    x
-})
-
-setMethod("end", "hasGRanges", function(x, ...) {
-    end(x@gr, ...)
-})
-setReplaceMethod("end", "hasGRanges", function(x, check = TRUE, value) {
-    end(x@gr, check = check) <- value
-    x
-})
-
-setMethod("width", "hasGRanges", function(x) {
-    width(x@gr)
-})
-setReplaceMethod("width", "hasGRanges", function(x, check = TRUE, value) {
-    width(x@gr, check = check) <- value
-    x
-})
-
-setMethod("strand", "hasGRanges", function(x) {
-    strand(x@gr)
-})
-setReplaceMethod("strand", "hasGRanges", function(x, value) {
-    strand(x@gr) <- value
-    x
-})
-
-setMethod("length", "hasGRanges", function(x) length(x@gr))
-
-setMethod("[", "hasGRanges", function(x, i, ...) {
-    if(missing(i))
-        stop("need [i] for subsetting")
-    if(missing(i))
-        return(x)
-    x@gr <- x@gr[i]
-    x
-})
-
-setMethod("findOverlaps",
-          signature(query = "hasGRanges", subject = "GenomicRanges"),
-          function (query, subject, maxgap = -1L, minoverlap = 0L,
-                    type = c("any", "start", "end", "within", "equal"),
-                    select = c("all", "first", "last", "arbitrary"),
-                    ignore.strand = FALSE, ...) {
-              findOverlaps(query = query@gr, subject = subject,
-                           maxgap = maxgap, minoverlap = minoverlap,
-                           type = match.arg(type), select = match.arg(select),
-                           ignore.strand = ignore.strand, ...)
-          })
-
-setMethod("findOverlaps",
-          signature(query = "GenomicRanges", subject = "hasGRanges"),
-          function (query, subject, maxgap = -1L, minoverlap = 0L,
-                    type = c("any", "start", "end", "within", "equal"),
-                    select = c("all", "first", "last", "arbitrary"),
-                    ignore.strand = FALSE, ...) {
-              findOverlaps(query = query, subject = subject@gr,
-                           maxgap = maxgap, minoverlap = minoverlap,
-                           type = match.arg(type), select = match.arg(select),
-                           ignore.strand = ignore.strand, ...)
-          })
-
-setMethod("findOverlaps",
-          signature(query = "hasGRanges", subject = "hasGRanges"),
-          function (query, subject, maxgap = -1L, minoverlap = 0L,
-                    type = c("any", "start", "end", "within", "equal"),
-                    select = c("all", "first", "last", "arbitrary"),
-                    ignore.strand = FALSE, ...) {
-              findOverlaps(query = query@gr, subject = subject@gr,
-                           maxgap = maxgap, minoverlap = minoverlap,
-                           type = match.arg(type), select = match.arg(select),
-                           ignore.strand = ignore.strand, ...)
-          })
-
-setMethod("overlapsAny", c("hasGRanges", "GenomicRanges"),
-    IRanges:::default_overlapsAny
-)
-setMethod("overlapsAny", c("GenomicRanges", "hasGRanges"),
-    IRanges:::default_overlapsAny
-)
-setMethod("overlapsAny", c("hasGRanges", "hasGRanges"),
-    IRanges:::default_overlapsAny
-)
-
-setMethod("subsetByOverlaps", c("hasGRanges", "GenomicRanges"),
-    IRanges:::default_subsetByOverlaps
-)
-setMethod("subsetByOverlaps", c("GenomicRanges", "hasGRanges"),
-    IRanges:::default_subsetByOverlaps
-)
-setMethod("subsetByOverlaps", c("hasGRanges", "hasGRanges"),
-    IRanges:::default_subsetByOverlaps
-)
-
diff --git a/man/BSseqStat-class.Rd b/man/BSseqStat-class.Rd
index cc26fd1..79b8877 100644
--- a/man/BSseqStat-class.Rd
+++ b/man/BSseqStat-class.Rd
@@ -17,9 +17,11 @@
 }
 \arguments{
     \item{gr}{The genomic locations as an object of class \code{GRanges}.}
-    \item{stats}{The statistics, as a list of matrix-like objects (see
-        'Details' below).}
-    \item{parameters}{A list of parameters.}
+    \item{stats}{A list of matrix-like objects (see 'Details' below) with
+      list elements representing various statistics for methylation loci
+      along the genome.}
+    \item{parameters}{A list of parameters, as an object of class \code{list},
+      representing how the statistics were computed.}
 }
 \details{
     The matrix-like elements of the list in the 'stats' slot will be
@@ -35,19 +37,8 @@
     However, usually objects are returned by \code{BSmooth.fstat(...)} and
     not constructed by the user.
 }
-\section{Slots}{
-  \describe{
-    \item{\code{stats}:}{This is a list of   \code{\link[DelayedArray]{DelayedMatrix}}
-      objects with list elements representing various statistics for
-      methylation loci along the genome.}
-    \item{\code{parameters}:}{Object of class \code{list}.  A list of
-      parameters representing how the statistics were computed.}
-    \item{\code{gr}:}{Object of class \code{GRanges} giving genomic
-      locations.}
-  }
-}
 \section{Extends}{
-    Class \code{\linkS4class{hasGRanges}}, directly.
+    Class \code{\link[GenomicRanges]{GRanges}}, directly.
 }
 \section{Methods}{
     \describe{
@@ -57,10 +48,11 @@
     }
 }
 \section{Utilities}{
-    This class extends \code{hasGRanges} and therefore inherits a number
-    of useful \code{GRanges} methods that operate on the \code{gr} slot,
-    used for accessing and setting the genomic locations and also do
-    \code{subsetByOverlaps}.
+    This class extends \code{\link[GenomicRanges]{GRanges}} and therefore
+    inherits the full \code{GRanges} API. This means that \code{BSseqStat}
+    objects support any operation supported by \code{GRanges} objects, like
+    \code{seqnames}, \code{start}, \code{end}, \code{width}, \code{strand},
+    \code{[}, \code{findOverlaps}, \code{subsetByOverlaps}, etc...
 }
 \section{Coercion}{
   Package version 1.11.1 introduced a new version of representing
@@ -71,7 +63,8 @@
     Kasper Daniel Hansen \email{khansen@jhsph.edu}
 }
 \seealso{
-    \code{\linkS4class{hasGRanges}} for accessing the genomic locations.
+    \code{\link[GenomicRanges]{GRanges}} in the \pkg{GenomicRanges} package
+    for accessing the genomic locations.
     \code{\link{BSmooth.fstat}} for a function
     that returns objects of class \code{BSseqStat}, and \code{\link{smoothSds}},
     \code{\link{computeStat}} and \code{\link{dmrFinder}}
diff --git a/man/BSseqTstat-class.Rd b/man/BSseqTstat-class.Rd
index 4b17db5..a5af22a 100644
--- a/man/BSseqTstat-class.Rd
+++ b/man/BSseqTstat-class.Rd
@@ -17,8 +17,11 @@
 }
 \arguments{
   \item{gr}{The genomic locations as an object of class \code{GRanges}.}
-  \item{stats}{The statistics, as a matrix-like object (see 'Details' below).}
-  \item{parameters}{A list of parameters.}
+  \item{stats}{A matrix-like object (see 'Details' below) with columns
+    representing various statistics for methylation loci along the
+    genome.}
+  \item{parameters}{A list of parameters, as an object of class \code{list},
+    representing how the t-statistics were computed.}
 }
 
 \details{
@@ -35,20 +38,8 @@ Objects can be created by calls of the form \code{BSseqTstat(...)}.
 However, usually objects are returned by \code{BSmooth.tstat(...)} and
 not constructed by the user..
 }
-\section{Slots}{
-  \describe{
-    \item{\code{stats}:}{This is a
-      \code{\link[DelayedArray]{DelayedMatrix}} object with columns
-      representing  various statistics for methylation loci along the
-      genome.}
-    \item{\code{parameters}:}{Object of class \code{list}.  A list of
-      parameters representing how the t-statistics were computed.}
-    \item{\code{gr}:}{Object of class \code{GRanges} giving genomic
-      locations.}
-  }
-}
 \section{Extends}{
-Class \code{\linkS4class{hasGRanges}}, directly.
+Class \code{\link[GenomicRanges]{GRanges}}, directly.
 }
 \section{Methods}{
   \describe{
@@ -58,10 +49,11 @@ Class \code{\linkS4class{hasGRanges}}, directly.
   }
 }
 \section{Utilities}{
-  This class extends \code{hasGRanges} and therefore inherits a number
-  of useful \code{GRanges} methods that operate on the \code{gr} slot,
-  used for accessing and setting the genomic locations and also do
-  \code{subsetByOverlaps}.
+  This class extends \code{\link[GenomicRanges]{GRanges}} and therefore
+  inherits the full \code{GRanges} API. This means that \code{BSseqTstat}
+  objects support any operation supported by \code{GRanges} objects, like
+  \code{seqnames}, \code{start}, \code{end}, \code{width}, \code{strand},
+  \code{[}, \code{findOverlaps}, \code{subsetByOverlaps}, etc...
   }
 \section{Coercion}{
   Package version 1.11.1 introduced a new version of representing
@@ -72,8 +64,9 @@ Class \code{\linkS4class{hasGRanges}}, directly.
   Kasper Daniel Hansen \email{khansen@jhsph.edu}
 }
 \seealso{
-  The package vignette(s).  \code{\linkS4class{hasGRanges}} for accessing
-  the genomic locations.  \code{\link{BSmooth.tstat}} for a function
+  The package vignette(s).  \code{\link[GenomicRanges]{GRanges}} in the
+  \pkg{GenomicRanges} package for accessing the genomic locations.
+  \code{\link{BSmooth.tstat}} for a function
   that returns objects of class \code{BSseqTstat}, and \code{\link{dmrFinder}}
   for a function that computes DMRs based on the t-statistics.  Also see
   \code{\link[bsseqData]{BS.cancer.ex.tstat}} for an example of the
@@ -82,6 +75,7 @@ Class \code{\linkS4class{hasGRanges}}, directly.
 \examples{
 if(require(bsseqData)) {
     data(BS.cancer.ex.tstat)
+    BS.cancer.ex.tstat <- updateObject(BS.cancer.ex.tstat)
     dmrFinder(BS.cancer.ex.tstat)
 }
 }
diff --git a/man/dmrFinder.Rd b/man/dmrFinder.Rd
index 55ac408..657020c 100644
--- a/man/dmrFinder.Rd
+++ b/man/dmrFinder.Rd
@@ -71,6 +71,7 @@ dmrFinder(bstat, cutoff = NULL, qcutoff = c(0.025, 0.975),
 }
 \examples{
 if(require(bsseqData)) {
+  BS.cancer.ex.tstat <- updateObject(BS.cancer.ex.tstat)
   dmrs0 <- dmrFinder(BS.cancer.ex.tstat, cutoff = c(-4.6, 4.6), verbose = TRUE)
   dmrs <- subset(dmrs0, abs(meanDiff) > 0.1 & n >= 3)
 }
diff --git a/man/getStats.Rd b/man/getStats.Rd
index ba912ac..a234e45 100644
--- a/man/getStats.Rd
+++ b/man/getStats.Rd
@@ -39,6 +39,7 @@ getStats(bstat, regions = NULL, ...)
 \examples{
 if(require(bsseqData)) {
   data(BS.cancer.ex.tstat)
+  BS.cancer.ex.tstat <- updateObject(BS.cancer.ex.tstat)
   head(getStats(BS.cancer.ex.tstat))
   reg <- GRanges(seqnames = c("chr22", "chr22"),
      ranges = IRanges(start = c(1, 2*10^7), end = c(2*10^7 +1, 4*10^7)))
diff --git a/man/hasGRanges-class.Rd b/man/hasGRanges-class.Rd
deleted file mode 100644
index 1a3bdbe..0000000
--- a/man/hasGRanges-class.Rd
+++ /dev/null
@@ -1,99 +0,0 @@
-\name{hasGRanges-class}
-\Rdversion{1.1}
-\docType{class}
-\alias{class:hasGRanges}
-\alias{hasGRanges-class}
-\alias{hasGRanges}
-\alias{seqnames,hasGRanges-method}
-\alias{seqnames<-,hasGRanges-method}
-\alias{seqlevels,hasGRanges-method}
-\alias{seqlevels<-,hasGRanges-method}
-\alias{seqlengths,hasGRanges-method}
-\alias{seqlengths<-,hasGRanges-method}
-\alias{granges,hasGRanges-method}
-\alias{start,hasGRanges-method}
-\alias{start<-,hasGRanges-method}
-\alias{end,hasGRanges-method}
-\alias{end<-,hasGRanges-method}
-\alias{width,hasGRanges-method}
-\alias{width<-,hasGRanges-method}
-\alias{strand,hasGRanges-method}
-\alias{strand<-,hasGRanges-method}
-\alias{strand<-,hasGRanges,ANY-method}
-\alias{length,hasGRanges-method}
-\alias{[,hasGRanges-method}
-\alias{[,hasGRanges,ANY,ANY,ANY-method}
-\alias{findOverlaps,hasGRanges,GenomicRanges-method}
-\alias{findOverlaps,GenomicRanges,hasGRanges-method}
-\alias{findOverlaps,hasGRanges,hasGRanges-method}
-\alias{overlapsAny,hasGRanges,GenomicRanges-method}
-\alias{overlapsAny,GenomicRanges,hasGRanges-method}
-\alias{overlapsAny,hasGRanges,hasGRanges-method}
-\alias{subsetByOverlaps,hasGRanges,GenomicRanges-method}
-\alias{subsetByOverlaps,GenomicRanges,hasGRanges-method}
-\alias{subsetByOverlaps,hasGRanges,hasGRanges-method}
-
-\title{Class hasGRanges}
-\description{
-  A class with a GRanges slot, used as a building block for other
-  classes.  Provides basic accessor functions etc.
-}
-\section{Objects from the Class}{
-Objects can be created by calls of the form \code{new("hasGRanges", ...)}.
-}
-\section{Slots}{
-  \describe{
-    \item{\code{gr}:}{Object of class \code{GRanges}.}
-  }
-}
-\section{Methods}{
-  \describe{
-    \item{"["}{Subsets a single dimension.}
-    \item{granges}{Get the \code{GRanges} object representing 
-      genomic locations.}
-    \item{start,start<-,end,end<-,width,width<-}{Start, end and width
-      for the genomic locations of the object, also replacement
-      functions.  This accessor functions operate directly on the
-      \code{gr} slot.} 
-    \item{strand,strand<-}{Getting and setting the
-      \code{strand} of the genomic locations (the \code{gr} slot).} 
-    \item{seqlengths,seqlengths<-}{Getting and setting the
-      \code{seqlengths} of the genomic locations (the \code{gr} slot).} 
-    \item{seqlevels,seqlevels<-}{Getting and setting the
-      \code{seqlevels} of the genomic locations (the \code{gr} slot).} 
-    \item{seqnames,seqnames<-}{Getting and setting the
-      \code{seqnames} of the genomic locations (the \code{gr} slot).} 
-    \item{show}{The show method.}
-    \item{findOverlaps}{\code{(query = "hasGRanges", subject =
-	"hasGRanges")}: finds overlaps between the \code{granges()} of
-      the two objects.}
-    \item{findOverlaps}{\code{(query = "GenomicRanges", subject =
-	"hasGRanges")}: finds overlaps between query and the \code{granges()} of
-      the subject.}
-    \item{findOverlaps}{\code{(query = "hasGRanges", subject =
-	"GenomicRanges")}: finds overlaps between the \code{granges()}
-      of the query and the subject.}
-    \item{subsetByOverlaps}{\code{(query = "hasGRanges", subject =
-	"hasGRanges")}: Subset the query, keeping the genomic locations that 
-      overlaps the subject.}
-    \item{subsetByOverlaps}{\code{(query = "hasGRanges", subject =
-	"GenomicRanges")}: Subset the query, keeping the genomic
-      locations that overlaps the subject.}
-    \item{subsetByOverlaps}{\code{(query = "GenomicRanges",
-	subject = "hasGRanges")}: Subset the query, keeping the genomic
-      locations that overlaps the subject.}
-  }
-}
-\author{
-  Kasper Daniel Hansen \email{khansen@jhsph.edu}
-}
-\note{
-  If you extend the \code{hasGRanges} class, you should consider writing
-  a subset method (\code{[}), and a \code{show} method.  If the new
-  class supports single index subsetting, the \code{subsetByOverlaps}
-  methods will automatically extend.
-}
-\examples{
-showClass("hasGRanges")
-}
-\keyword{classes}
diff --git a/man/internals.Rd b/man/internals.Rd
deleted file mode 100644
index 4f5edbd..0000000
--- a/man/internals.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-\name{Internals}
-\alias{matrixOrNULL-class}
-\title{Internals}
-\description{
-   The \code{matrixOrNULL} class is a class union, representing a slot
-   which is either a matrix or \code{NULL} (representing missing
-   information). 
-}
-\value{
-  Undocumented
-}
-\keyword{internal}