@@ -1996,113 +1996,11 @@ UcscTrack <- function(track, table = NULL, trackType = c(

 ## AlignedReadTrack ----------------------------------------------------------------------------------------------------

-##

-## AlignedReadTrack: A track to visualize sequence reads, as typically produced by NGS experiments

-##

-## Slots: no additional formal slots are defined

-## A bunch of DisplayPars are set during object instantiation:

-##    o detail: the amount of plotting details to show for the aligned reads, one in c("reads", "coverage")

-

-setClass("AlignedReadTrack",

-    representation = representation(

-        coverage = "list",

-        coverageOnly = "logical"

-    ),

-    contains = "StackedTrack",

-    prototype = prototype(

-        stacking = "squish",

-        name = "AlignedReadTrack",

-        coverageOnly = FALSE,

-        dp = DisplayPars(

-            detail = "coverage",

-            type = "histogram",

-            fill = "#0080ff",

-            size = NULL,

-            collapse = FALSE

-        )

-    )

-)

-

-## Recompute coverage on plus and minus strand and combined strands for AlignedRead tracks

-## and update the respective slot to hold this information

-setMethod("setCoverage", signature("AlignedReadTrack"),

-    definition = function(GdObject) {

-        if (length(GdObject)) {

-            str <- factor(strand(GdObject), levels = c("+", "-"))

-            gdSplit <- as.list(split(range(GdObject), str))

-            covs <- lapply(gdSplit, coverage)

-            covs[["*"]] <- coverage(range(GdObject))

-            GdObject@coverage <- covs

-        }

-        return(GdObject)

-    }

-)

-

-## Essentially we just update the display parameters here and precompute the coverage

-setMethod("initialize", "AlignedReadTrack", function(.Object, coverageOnly = FALSE, ...) {

-    ## the diplay parameter defaults

-    .makeParMapping()

-    .Object <- .updatePars(.Object, "AlignedReadTrack")

-    .Object <- callNextMethod(.Object, ...)

-    .Object <- setCoverage(.Object)

-    if (coverageOnly) {

-        ## from <- min(unlist(lapply(.Object@coverage, function(y) if(length(y)) min(start(y)))))

-        ## to <- max(unlist(lapply(.Object@coverage, function(y) if(length(y)) max(end(y)))))

-        from <- min(start(range(.Object)))

-        to <- max(end(range(.Object)))

-        .Object@range <- GRanges(

-            ranges = IRanges(start = from, end = to),

-            strand = names(.Object@coverage), seqnames = .Object@chromosome

-        )

-        .Object@coverageOnly <- coverageOnly

-    }

-    return(.Object)

-})

-

-## Constructor. The following arguments are supported:

-##    o range: a data.frame or a GRanges object containing the information

-##       about the track items. If a data.frame, it needs to be coerceable

-##     to a GRanges object, i.e., it needs at least the mandatory 'start', 'stop' and

-##     'strand' columns.

-##    Instead of using the 'range' parameter, all these values can also be passed as

-##    individual vectors, in which case they need to be of similar length.

-##    o start, end, width: numeric vectors of the item start and end coordinates, or their widths

-##    o strand: the strand information needs to be provided in the form '+' for

-##       the Watson strand, '-' for the Crick strand.

-##    o genome, chromosome: the reference genome and active chromosome for the track.

-##    o stacking: character controlling the stacking of overlapping items. One in 'hide',

-##       'dense', 'squish', 'pack' or 'full'.

-##    o name: the name of the track. This will be used for the title panel.

-## All additional items in ... are being treated as further DisplayParameters

-## (N)

-AlignedReadTrack <- function(range = NULL, start = NULL, end = NULL, width = NULL, chromosome, strand, genome, stacking = "squish",

-                             name = "AlignedReadTrack", coverageOnly = FALSE, ...) {

-    .Deprecated("AlignmentsTrack")

-    .missingToNull(c("strand", "chromosome", "genome"))

-    ## Build a GRanges object from the inputs

-    range <- .buildRange(

-        range = range, start = start, end = end, width = width,

-        args = list(strand = strand, genome = genome, chromosome = chromosome),

-        defaults = list(strand = "+", genome = NA, chromosome = "chrNA"), chromosome = chromosome,

-        trackType = "AlignedReadTrack"

-    )

-    str <- unique(as.character(GenomicRanges::strand(range)))

-    if ("*" %in% str) {

-        stop("Only '+' and '-' strand information is allowed for AlignedReadTrack objects.")

-    }

-    if (missing(chromosome) || is.null(chromosome)) {

-        chromosome <- if (length(range) > 0) .chrName(as.character(seqnames(range)[1])) else "chrNA"

-    }

-    ## And finally the object instantiation

-    return(new("AlignedReadTrack",

-        chromosome = chromosome, range = range, name = name, genome = genome(range)[1],

-        stacking = stacking, coverageOnly = coverageOnly, ...

-    ))

+AlignedReadTrack <- function() {

+    .Defunct("AlignmentsTrack")

 }

-

-

 ## SequenceTrack -------------------------------------------------------------------------------------------------------

 ##

 ## SequenceTrack: A generic track to visualize nucleotide sequences. This class is virtual.

deleted file mode 100644

@@ -1,1368 +0,0 @@

-\name{AlignedReadTrack-class}

-\Rdversion{1.1}

-\docType{class}

-\alias{AlignedReadTrack-class}

-\alias{AlignedReadTrack}

-\alias{[,AlignedReadTrack-method}

-\alias{[,AlignedReadTrack,ANY,ANY-method}

-\alias{[,AlignedReadTrack,ANY,ANY,ANY-method}

-\alias{coverage,AlignedReadTrack-method}

-\alias{drawAxis,AlignedReadTrack-method}

-\alias{drawGD,AlignedReadTrack-method}

-\alias{drawGrid,AlignedReadTrack-method}

-\alias{initialize,AlignedReadTrack-method}

-\alias{setCoverage,AlignedReadTrack-method}

-\alias{show,AlignedReadTrack-method}

-\alias{split,AlignedReadTrack,ANY-method}

-\alias{split,AlignedReadTrack-method}

-\alias{subset,AlignedReadTrack-method}

-

-\title{DEPRECATED! AlignedReadTrack class and methods)}

-

-\description{

-  

-  DEPRECATED! This class and methods are deprecated, please use \code{DataTrack}, 

-  \code{AnnotationTrack} or \code{AlignmentsTrack} instead.

-  

-  A class to represent short sequences that have been aligned to a

-  reference genome as they are typically generated in a next generation

-  sequencing experiment.

-

-}

-

-\section{Objects from the Class}{

-

-  Objects can be created using the constructor function \code{AlignedReadTrack}.

-

-}

-

-

-\usage{

-

-AlignedReadTrack(range=NULL, start=NULL, end=NULL, width=NULL, chromosome, strand, genome,

-stacking="squish", name="AlignedReadTrack", coverageOnly=FALSE, ...)

-

-}

-

-\arguments{

-

-  \item{range}{An object of class \code{\linkS4class{GRanges}}, or a

-    \code{data.frame} which will be coerced into one in which case it

-    needs to contain at least the three columns:

-

-    \describe{

-

-      \item{}{\code{start}, \code{end}: the start and end coordinates

-    for the track items.}

-

-      \item{}{\code{strand}: the strand information for the track

-    items. It may be provided in the form \code{+} for the Watson

-    strand, \code{-} for the Crick strand or \code{*} for either one

-    of the two.}

-

-    }

-

-    Alternatively, the \code{range} argument may be missing, in which

-    case the relevant information has to be provided as individual

-    function arguments (see below).

-

-  }

-

-  \item{start, end, width}{Integer vectors, giving the start and the end

-    end coordinates for the individual track items, or their width. Two

-    of the three need to be specified, and have to be of equal length or

-    of length one, in which case this value will be recycled. Otherwise,

-    the usual R recycling rules for vectors do not apply.}

-

-  \item{strand}{Character vector, the strand information for the

-    individual track items.  Needs to be of equal length as the

-    \code{start, end} or \code{width} vectors, or of length 1. Please

-    note that grouped items need to be on the same strand, and erroneous

-    entries will result in casting of an error.}

-

-  \item{chromosome}{The chromosome on which the track's genomic ranges

-    are defined. A valid UCSC chromosome identifier. Please note that at

-    this stage only syntactic checking takes place, i.e., the argument

-    value needs to be a single integer, numeric character or a character

-    of the form \code{chrx}, where \emph{x} may be any

-    possible string. The user has to make sure that the respective

-    chromosome is indeed defined for the the track's genome.}

-

-  \item{genome}{The genome on which the track's ranges are

-    defined. Usually this is a valid UCSC genome identifier, however

-    this is not being formally checked at this point.}

-

-  \item{stacking}{The stacking type for overlapping items of the

-    track. One in \code{c(hide, dense, squish, pack,full)}. Currently,

-    only hide (don't show the track items, squish (make best use of the

-    available space) and dense (no stacking at all) are implemented.}

-

-  \item{name}{Character scalar of the track's name used in the title

-    panel when plotting.}

-

-  \item{coverageOnly}{Instead of storing individual reads, just compute

-    the coverage and store the resulting coverage vector.}

-

-  \item{\dots}{Additional items which will all be interpreted as further

-    display parameters.}

-

-}

-

-\value{

-

-  The return value of the constructor function is a new object of class

-  \code{AlignedReadTrack}.

-

-}

-

-\section{Slots}{

-

-  \describe{

-

-    \item{\code{coverage}:}{Object of class \code{"list"}, a list of

-      coverage vectors for the plus strand, the minus strand and for

-      both strands combined.}

-

-    \item{\code{coverageOnly}:}{Object of class \code{"logical"}, flag

-      to determine whether the object stores read locations or the coverage

-      vectors only.}

-

-     \item{\code{stacking}:}{Object of class \code{"character"},

-      inherited from class \code{\linkS4class{StackedTrack}}}

-

-    \item{\code{stacks}:}{Object of class \code{"environment"},

-      inherited from class \code{\linkS4class{StackedTrack}}}

-

-    \item{\code{range}:}{Object of class \code{\linkS4class{GRanges}},

-      inherited from class \code{\linkS4class{RangeTrack}}}

-

-    \item{\code{chromosome}:}{Object of class \code{"character"},

-      inherited from class \code{\linkS4class{RangeTrack}} }

-

-    \item{\code{genome}:}{Object of class \code{"character"}, inherited

-      from class \code{\linkS4class{RangeTrack}}}

-

-    \item{\code{dp}:}{Object of class

-      \code{\linkS4class{DisplayPars}}, inherited from class

-      \code{\linkS4class{GdObject}} }

-

-    \item{\code{name}:}{Object of class \code{"character"}, inherited

-      from class \code{\linkS4class{GdObject}}}

-

-    \item{\code{imageMap}:}{Object of class

-      \code{\linkS4class{ImageMap}}, inherited from class

-      \code{\linkS4class{GdObject}}}

-

-  }

-}

-

-\section{Extends}{

-

-  Class \code{"\linkS4class{StackedTrack}"}, directly.

-

-  Class \code{"\linkS4class{RangeTrack}"}, by class "StackedTrack",

-  distance2.

-

-  Class \code{"\linkS4class{GdObject}"}, by class "StackedTrack",

-  distance3.

-

-}

-

-\section{Methods}{

-

-  In the following code chunks, \code{obj} is considered to be an object

-  of class \code{AlignedReadTrack}.

-

-  \bold{\emph{Exported in the name space:}}

-

-  \describe{

-

-    \item{[}{\code{signature(x="AlignedReadTrack")}: subset the items in

-      the \code{AlignedReadTrack}. This is essentially similar to

-      subsetting of the \code{\linkS4class{GRanges}} object in the

-      \code{range} slot. For most applications, the \code{subset} method

-      may be more appropriate. The operation is only supported for

-      objects that still contain all the read locations, i.e.,

-      \code{coverageOnly=FALSE}.

-

-      \emph{Additional Arguments:}

-

-      \describe{

-

-    \item{}{\code{i}: subsetting indices}

-

-      }

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{obj[1:5]}}

-

-      }

-    }

-

-    \item{subset}{\code{signature(x="AlignedReadTrack")}: subset a

-      \code{AlignedReadTrack} by coordinates and sort if necessary.

-

-      \emph{Usage:}

-

-      \code{subset(x, from, to, sort=FALSE, stacks=FALSE)}

-

-      \emph{Additional Arguments:}

-

-      \describe{

-

-    \item{}{\code{from}, \code{to}: the coordinates range to subset

-      to.}

-

-    \item{}{\code{sort}: sort the object after subsetting. Usually

-      not necessary.}

-

-    \item{}{\code{stacks}: recompute the stacking after subsetting

-      which can be expensive and is not always necessary.}

-

-      }

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{subset(obj, from=10, to=20)}}

-

-    \item{}{\code{subset(obj, from=10, to=20, sort=TRUE, stacks=FALSE)}}

-

-      }

-    }

-

-    \item{split}{\code{signature(x="AlignedReadTrack")}: split an

-      \code{AlignedReadTrack} object by an appropriate factor vector (or

-      another vector that can be coerced into one). The output of this

-      operation is a list of \code{AlignedReadTrack} objects.

-

-      \emph{Additional Arguments:}

-

-      \describe{

-

-    \item{}{\code{f}: the splitting factor.}

-

-    \item{}{\code{\dots}: all further arguments are ignored.}

-

-      }

-

-      \emph{Usage:}

-

-      \code{split(x, f, ...)}

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{split(obj, c("a", "a", "b", "c", "a"))}}

-

-      }

-    }

-

-    \item{coverage}{\code{signature(x="AlignedReadTrack")}: return the

-      coverage vector for one of the strands, or the combined vector.

-

-      \emph{Usage:}

-

-      \code{coverage(x, strand="*")}

-

-      \emph{Additional Arguments:}

-

-      \describe{

-

-    \item{}{\code{strand}: the selector for the strand, \code{+} for

-      the Watson strand, \code{-} for the Crick strand or \code{*}

-      for both strands.}

-

-      }

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{coveraget(obj)}}

-

-    \item{}{\code{coverage(obj, strand="-")}}

-

-      }

-    }

-  }

-

-  \bold{\emph{Internal methods:}}

-

-  \describe{

-

-

-    \item{setCoverage}{\code{signature(GdObject="AlignedReadTrack")}:

-      recompute the coverage on the plus and minus strand as well as for

-      the combined strands and update the respective slot.

-

-      \emph{Usage:}

-

-      \code{setCoverage(GdObject)}

-

-       \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{setCoverage(obj)}}

-

-      }

-    }

-

-    \item{drawAxis}{\code{signature(GdObject="AlignedReadTrack")}: add a y-axis

-      to the title panel of a track.

-

-      \emph{Usage:}

-

-      \code{drawAxis(GdObject, from, to, subset=FALSE, ...)}

-

-      \emph{Additional Arguments:}

-

-      \describe{

-

-    \item{}{\code{from}, \code{to}: compute axis range from the data

-      within a certain coordinates range only.}

-

-    \item{}{\code{subset}: subset the object prior to calculating

-      the axis ranges. Can be expensive and is not always needed.}

-

-    \item{}{\code{\dots}: all further arguments are ignored.}

-

-      }

-

-      \emph{Examples:}

-

-      \describe{

-

-          \item{}{\code{Gviz:::drawAxis(obj)}}

-

-      }

-    }

-

-    \item{drawGD}{\code{signature(gdObject="AlignedReadTrack")}: plot the

-      object to a graphics device. The return value of this method is

-      the input object, potentially updated during the plotting

-      operation. Internally, there are two modes in which the method can

-      be called. Either in 'prepare' mode, in which case no plotting is

-      done but the object is preprocessed based on the

-      available space, or in 'plotting' mode, in which case the actual

-      graphical output is created. Since subsetting of the object can be

-      potentially costly, this can be switched off in case subsetting

-      has already been performed before or is not necessary.

-

-      \emph{Usage:}

-

-      \code{drawGD(GdObject, minBase, maxBase, prepare=FALSE,

-    subset=TRUE, ...)}

-

-      \emph{Additional Arguments:}

-

-      \describe{

-

-    \item{}{\code{minBase}, \code{maxBase}: the coordinate range to

-      plot.}

-

-    \item{}{\code{prepare}: run method in preparation or in

-      production mode.}

-

-    \item{}{\code{subset}: subset the object to the visible region

-    or skip the potentially expensive subsetting operation.}

-

-    \item{}{\code{\dots}: all further arguments are ignored.}

-

-      }

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{Gviz:::drawGD(obj)}}

-

-    \item{}{\code{Gviz:::drawGD(obj, minBase=1, maxBase=100)}}

-

-    \item{}{\code{Gviz:::drawGD(obj, prepare=TRUE,

-        subset=FALSE)}}

-

-      }

-    }

-

-    \item{drawGrid}{\code{signature(GdObject="AlignedReadTrack")}: superpose a grid on top of a track.

-

-      \emph{Usage:}

-

-      \code{drawGrid(GdObject, from, to)}

-

-      \emph{Additional Arguments:}

-

-      \describe{

-

-    \item{}{\code{from}, \code{to}: draw grid within a certain

-      coordinates range. This needs to be supplied for the plotting

-      function to know the current genomic coordinates.}

-

-      }

-

-      \emph{Examples:}

-

-      \describe{

-

-          \item{}{\code{Gviz:::drawGrid(obj, from=10, to=100)}}

-

-      }

-    }

-

-

-    \item{initialize}{\code{signature(.Object="AligendReadTrack")}:

-      initialize the object.}

-

-    \item{show}{\code{signature(object="AlignedReadTrack")}: show a

-      human-readable summary of the object.}

-

-  }

-

-  \bold{\emph{Inherited methods:}}

-

-  \describe{

-

-    \item{stacking}{\code{signature(GdObject="AlignedReadTrack")}: return

-      the current stacking type.

-

-      \emph{Usage:}

-

-      \code{stacking(GdObject)}

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{stacking(obj)}}

-

-      }

-    }

-

-    \item{stacking<-}{\code{signature(GdObject="AlignedReadTrack",

-      value="character")}: set the object's stacking type to one in

-      \code{c(hide, dense, squish, pack,full)}.

-

-      \emph{Usage:}

-

-      \code{stacking<-(GdObject, value)}

-

-      \emph{Additional Arguments:}

-

-    \describe{

-

-      \item{}{\code{value}: replacement value.}

-

-    }

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{stacking(obj) <- "squish" }}

-

-      }

-    }

-

-    \item{setStacks}{\code{signature(GdObject="AlignedReadTrack")}:

-      recompute the stacks based on the available space and on the

-      object's track items and stacking settings.

-

-      \emph{Usage:}

-

-      \code{setStacks(GdObject, from, to)}

-

-      \emph{Additional Arguments:}

-

-      \describe{

-

-    \item{}{\code{from}, \code{to}: compute stacking within a

-      certain coordinates range. This needs to be supplied for the

-      plotting function to know the current genomic coordinates.}

-

-      }

-

-      \emph{Examples:}

-

-      \describe{

-

-          \item{}{\code{Gviz:::setStacks(obj)}}

-

-      }

-    }

-

-    \item{stacks}{\code{signature(GdObject="AlignedReadTrack")}: return

-      the stack indices for each track item.

-

-      \emph{Usage:}

-

-      \code{stacks(GdObject)}

-

-      \emph{Examples:}

-

-      \describe{

-

-          \item{}{\code{Gviz:::stacks(obj)}}

-

-      }

-    }

-

-    \item{chromosome}{\code{signature(GdObject="AlignedReadTrack")}:

-      return the chromosome for which the track is defined.

-

-      \emph{Usage:}

-

-      \code{chromosome(GdObject)}

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{chromosome(obj)}}

-

-      }

-    }

-

-    \item{chromosome<-}{\code{signature(GdObject="AlignedReadTrack")}:

-      replace the value of the track's chromosome. This has to be a

-      valid UCSC chromosome identifier or an integer or character

-      scalar that can be reasonably coerced into one.

-

-      \emph{Usage:}

-

-      \code{chromosome<-(GdObject, value)}

-

-      \emph{Additional Arguments:}

-

-      \describe{

-

-    \item{}{\code{value}: replacement value.}

-

-      }

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{chromosome(obj) <- "chr12"}}

-

-      }

-    }

-

-    \item{start, end, width}{\code{signature(x="AlignedReadTrack")}: the

-      start or end coordinates of the track items, or their width in

-      genomic coordinates.

-

-      \emph{Usage:}

-

-      \code{start(x)}

-

-      \code{end(x)}

-

-      \code{width(x)}

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{start(obj)}}

-

-    \item{}{\code{end(obj)}}

-

-    \item{}{\code{width(obj)}}

-

-      }

-    }

-

-    \item{start<-, end<-, width<-}{\code{signature(x="AlignedReadTrack")}:

-      replace the start or end coordinates of the track items, or their

-      width.

-

-      \emph{Usage:}

-

-      \code{start<-(x, value)}

-

-      \code{end<-(x, value)}

-

-      \code{width<-(x, value)}

-

-      \emph{Additional Arguments:}

-

-    \describe{

-

-      \item{}{\code{value}: replacement value.}

-

-    }

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{start(obj) <- 1:10}}

-

-    \item{}{\code{end(obj) <- 20:30}}

-

-    \item{}{\code{width(obj) <- 1}}

-

-      }

-    }

-

-    \item{position}{\code{signature(GdObject="AlignedReadTrack")}: the

-      arithmetic mean of the track item's coordionates, i.e.,

-      \code{(end(obj)-start(obj))/2}.

-

-      \emph{Usage:}

-

-      \code{position(GdObject)}

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{position(obj)}}

-

-      }

-    }

-

-    \item{feature}{\code{signature(GdObject="AlignedReadTrack")}: return the

-      grouping information for track items. For certain sub-classes,

-      groups may be indicated by different color schemes when

-      plotting. See \code{\link{grouping}} or

-      \code{\linkS4class{AnnotationTrack}} and

-      \code{\linkS4class{GeneRegionTrack}} for details.

-

-      \emph{Usage:}

-

-      \code{feature(GdObject)}

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{feature(obj)}}

-

-      }

-    }

-

-    \item{feature<-}{\code{signature(gdObject="AlignedReadTrack",

-      value="character")}: set the grouping information for track

-      items. This has to be a factor vector (or another type of vector

-      that can be coerced into one) of the same length as the number of

-      items in the \code{AlignedReadTrack}. See \code{\link{grouping}} or

-      \code{\linkS4class{AnnotationTrack}} and

-      \code{\linkS4class{GeneRegionTrack}} for details.

-

-      \emph{Usage:}

-

-      \code{feature<-(GdObject, value)}

-

-      \emph{Additional Arguments:}

-

-      \describe{

-

-    \item{}{\code{value}: replacement value.}

-

-      }

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{feature(obj) <- c("a", "a", "b", "c", "a")}}

-

-      }

-    }

-

-    \item{genome}{\code{signature(x="AlignedReadTrack")}: return the track's genome.

-

-      \emph{Usage:}

-

-      \code{genome(x)}

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{genome(obj)}}

-

-      }

-    }

-

-    \item{genome<-}{\code{signature(x="AlignedReadTrack")}: set the track's

-      genome. Usually this has to be a valid UCSC identifier, however

-      this is not formally enforced here.

-

-      \emph{Usage:}

-

-      \code{genome<-(x, value)}

-

-      \emph{Additional Arguments:}

-

-      \describe{

-

-    \item{}{\code{value}: replacement value.}

-

-      }

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{genome(obj) <- "mm9"}}

-

-      }

-    }

-

-    \item{length}{\code{signature(x="AlignedReadTrack")}: return the number

-      of items in the track.

-

-      \emph{Usage:}

-

-      \code{length(x)}

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{length(obj)}}

-

-      }

-    }

-

-    \item{range}{\code{signature(x="AlignedReadTrack")}: return the genomic

-      coordinates for the track as an object of class

-      \code{\linkS4class{IRanges}}.

-

-      \emph{Usage:}

-

-      \code{range(x)}

-

-      \emph{Examples:}

-

-      \describe{

-

-    \item{}{\code{range(obj)}}

-

-      }

-    }

-

-    \item{ranges}{\code{signature(x="AlignedReadTrack")}: return the genomic

-      coordinates for the track along with all additional annotation

-      information as an object of class \code{\linkS4class{GRanges}}.

-

-      \emph{Usage:}

-

-      \code{ranges(x)}

-

-      \emph{Examples:}