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