AnnotationTrack-class   Class "AnnotationTrack"
BaseTrack-class         Class "BaseTrack" represents base specific data
DisplayPars             DisplayPars constructs objects of type
                        DisplayPars which are used to effect the
                        display of gdObjects
DisplayPars-class       Class "DisplayPars" is used to specify
                        graphical parameters to gdObjects.
ExonArray-class         Class "ExonArray" representing probe level exon
                        array data from Affymetrix
Gene-class              Class "Gene" represents the Ensembl Gene level
                        annotation
GeneModel-class         Class "GeneModel", represents a custom gene
                        model
GeneRegion-class        Class "GeneRegion", representing gene
                        structures in a defined genomic region
GenericArray-class      Class "GenericArray", representing array data
GenomeAxis-class        Class "GenomeAxis", representing a genomic
                        coordinate axis
HighlightRegion-class   Class "HighlightRegion" is used to highlight
                        vertical blocks of genomic regions.
Ideogram-class          Class "Ideogram", represent an Ideogram
ImplementsTrackOverlay-class
                        Class "ImplementsTrackOverlay"
Legend-class            Class "Legend", represents a legend to add to a
                        plot
MappedRead-class        Represents mapped reads
Overlay-class           Class "Overlay"
RectangleOverlay-class
                        Class "RectangleOverlay"
Segmentation-class      Class "Segmentation" is used to specify
                        segmentations to any class that extends
                        Segmentable (GenericArray, BaseTrack)
Smoothing-class         Class "Smoothing"
TextOverlay-class       Class "TextOverlay"
Title-class             Class "Title" representing the title of a plot
TrackOverlay-class      Class "TrackOverlay"
Transcript-class        Represent known transcript isoforms as annoted
                        by Ensembl
TranscriptRegion-class
                        Class "TranscriptRegion", representing a
                        genomic region with transcripts
cn                      Contains dummy copy number data
drawGD                  Generic called on each gdObject to do the
                        plotting.
drawTrackOverlay-methods
                        This method does the drawing of a track
                        overlay. One should implement this method to
                        gain track plotting functionality.
exonProbePos            Contains dummy exon probe positions
gdObject-class          Class "gdObject" is the parent class of all of
                        the objects in the system.
gdPlot                  gdPlot is the main plotting function of the
                        GenomeGraphs package
geneBiomart             AnnotationTrack objects from biomaRt
geneRegionBiomart       Construct an AnnotationTrack object from
                        biomaRt.
getGenomicRange         Retrieves the genomic range of an object
getPar                  Retrieves a display parameter from an object.
getSize                 gets the size
ideogramTab             Contains info to plot ideograms
intensity               Contains dummy intensity data
makeAnnotationTrack     Create objects of class AnnotationTrack
makeBaseTrack           Creates an object of class BaseTrack
makeExonArray           Creates and object of class ExonArray
makeGene                Creates an object of class Gene
makeGeneModel           Creates an object of class GeneModel
makeGeneRegion          Creates an object of class Gene containing the
                        intron-exon structures of genes
makeGenericArray        Creates an object of class GenericArray
makeGenomeAxis          Creates an object of class GenomeAxis
makeIdeogram            Creates object of class Ideogram
makeLegend              Creates an object of class Legend
makeRectangleOverlay    Create a rectangular overlay
makeSegmentation        Create objects of class segmentation
makeSmoothing           Create objects of class Smoothing
makeTextOverlay         Create objects of class TextOverlay
makeTitle               Creates an object of class Title
makeTranscript          Creates an object of class Transcript
probestart              Contains dummy expression array probe start
                        positions
segEnd                  Contains dummy copy number segmentation end
                        positions
segStart                Contains dummy copy number segmentation start
                        positions data
segments                Contains dummy copy number segment data
seqDataEx               This is an example data set from chromosome 4
                        of yeast from various publicly available
                        datasets.
setPar                  Sets a display parameter
showDisplayOptions      Print standard display options, DisplayPars for
                        an object or a class
unrData                 Contains exon array data
unrNProbes              Contains exon array data
unrPositions            Contains probe start and end positions of exon
                        array probes
yeastCons1              Contains dummy yeast conservation data
