Entry: AnnotationTrack-class
Aliases: AnnotationTrack-class drawGD,AnnotationTrack-method getPlotId,AnnotationTrack-method initialize,AnnotationTrack-method
Keywords: classes
Description: Class "AnnotationTrack"
URL: ../../../library/GenomeGraphs/html/AnnotationTrack-class.html

Entry: BaseTrack-class
Aliases: BaseTrack-class show,BaseTrack-method drawGD,BaseTrack-method
Keywords: classes
Description: Class "BaseTrack" represents base specific data
URL: ../../../library/GenomeGraphs/html/BaseTrack-class.html

Entry: DisplayPars-class
Aliases: DisplayPars-class initialize,DisplayPars-method show,DisplayPars-method getPar,DisplayPars-method setPar,DisplayPars-method
Keywords: classes
Description: Class "DisplayPars" is used to specify graphical parameters to gdObjects.
URL: ../../../library/GenomeGraphs/html/DisplayPars-class.html

Entry: DisplayPars
Aliases: DisplayPars
Keywords: hplot
Description: DisplayPars constructs objects of type DisplayPars which are used to effect the display of gdObjects
URL: ../../../library/GenomeGraphs/html/DisplayPars.html

Entry: ExonArray-class
Aliases: ExonArray-class show,ExonArray-method drawGD,ExonArray-method
Keywords: classes
Description: Class "ExonArray" representing probe level exon array data from Affymetrix
URL: ../../../library/GenomeGraphs/html/ExonArray-class.html

Entry: Gene-class
Aliases: Gene-class initialize,Gene-method drawGD,Gene-method show,Gene-method
Keywords: classes
Description: Class "Gene" represents the Ensembl Gene level annotation
URL: ../../../library/GenomeGraphs/html/Gene-class.html

Entry: GeneModel-class
Aliases: GeneModel-class drawGD,GeneModel-method
Keywords: classes
Description: Class "GeneModel", represents a custom gene model
URL: ../../../library/GenomeGraphs/html/GeneModel-class.html

Entry: GeneRegion-class
Aliases: GeneRegion-class initialize,GeneRegion-method show,GeneRegion-method drawGD,GeneRegion-method
Keywords: classes
Description: Class "GeneRegion", representing gene structures in a defined genomic region
URL: ../../../library/GenomeGraphs/html/GeneRegion-class.html

Entry: GenericArray-class
Aliases: GenericArray-class show,GenericArray-method drawGD,GenericArray-method
Keywords: classes
Description: Class "GenericArray", representing array data
URL: ../../../library/GenomeGraphs/html/GenericArray-class.html

Entry: GenomeAxis-class
Aliases: GenomeAxis-class drawGD,GenomeAxis-method
Keywords: classes
Description: Class "GenomeAxis", representing a genomic coordinate axis
URL: ../../../library/GenomeGraphs/html/GenomeAxis-class.html

Entry: HighlightRegion-class
Aliases: HighlightRegion-class
Keywords: classes
Description: Class "HighlightRegion" is used to highlight vertical blocks of genomic regions.
URL: ../../../library/GenomeGraphs/html/HighlightRegion-class.html

Entry: Ideogram-class
Aliases: Ideogram-class drawGD,Ideogram-method
Keywords: classes
Description: Class "Ideogram", represent an Ideogram
URL: ../../../library/GenomeGraphs/html/Ideogram-class.html

Entry: Legend-class
Aliases: Legend-class drawGD,Legend-method
Keywords: classes
Description: Class "Legend", represents a legend to add to a plot
URL: ../../../library/GenomeGraphs/html/Legend-class.html

Entry: MappedRead-class
Aliases: MappedRead-class show,MappedRead-method drawGD,MappedRead-method
Keywords: datasets
Description: Represents mapped reads
URL: ../../../library/GenomeGraphs/html/MappedRead-class.html

Entry: Overlay-class
Aliases: Overlay-class
Keywords: classes
Description: Class "Overlay"
URL: ../../../library/GenomeGraphs/html/Overlay-class.html

Entry: RectangleOverlay-class
Aliases: RectangleOverlay-class drawOverlay,RectangleOverlay-method
Keywords: classes
Description: Class "RectangleOverlay"
URL: ../../../library/GenomeGraphs/html/RectangleOverlay-class.html

Entry: Segmentable-class
Aliases: Segmentable-class getSegmentation,Segmentable-method
Keywords: classes
Description: Class "Segmentable"
URL: ../../../library/GenomeGraphs/html/Segmentable-class.html

Entry: Segmentation-class
Aliases: Segmentation-class getSegmentEnd,Segmentation-method getSegmentStart,Segmentation-method getSegments,Segmentation-method drawGD,Segmentation-method
Keywords: classes
Description: Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack)
URL: ../../../library/GenomeGraphs/html/Segmentation-class.html

Entry: TextOverlay-class
Aliases: TextOverlay-class drawOverlay, TextOverlay-method
Keywords: classes
Description: Class "TextOverlay"
URL: ../../../library/GenomeGraphs/html/TextOverlay-class.html

Entry: Title-class
Aliases: Title-class drawGD,Title-method
Keywords: classes
Description: Class "Title" representing the title of a plot
URL: ../../../library/GenomeGraphs/html/Title-class.html

Entry: Transcript-class
Aliases: Transcript-class initialize,Transcript-method show,Transcript-method drawGD,Transcript-method
Keywords: classes
Description: Represent known transcript isoforms as annoted by Ensembl
URL: ../../../library/GenomeGraphs/html/Transcript-class.html

Entry: TranscriptRegion-class
Aliases: TranscriptRegion-class show,TranscriptRegion-method
Keywords: classes
Description: Class "TranscriptRegion", representing a genomic region with transcripts
URL: ../../../library/GenomeGraphs/html/TranscriptRegion-class.html

Entry: cn
Aliases: cn
Keywords: datasets
Description: Contains dummy copy number data
URL: ../../../library/GenomeGraphs/html/cn.html

Entry: drawGD
Aliases: drawGD
Keywords: hplot
Description: Generic called on each gdObject to do the plotting.
URL: ../../../library/GenomeGraphs/html/drawGD.html

Entry: exonProbePos
Aliases: exonProbePos
Keywords: datasets
Description: Contains dummy exon probe positions
URL: ../../../library/GenomeGraphs/html/exonProbePos.html

Entry: gdObject-class
Aliases: gdObject-class getCex,gdObject-method getColor,gdObject-method getLty,gdObject-method getLwd,gdObject-method getPch,gdObject-method getPointSize,gdObject-method getSize,gdObject-method initialize,gdObject-method getPar,gdObject-method setPar,gdObject-method showDisplayOptions,gdObject-method showDisplayOptions,character-method
Keywords: classes
Description: Class "gdObject" is the parent class of all of the objects in the system.
URL: ../../../library/GenomeGraphs/html/gdObject-class.html

Entry: gdPlot
Aliases: gdPlot
Keywords: hplot
Description: gdPlot is the main plotting function of the GenomeGraphs package
URL: ../../../library/GenomeGraphs/html/gdPlot.html

Entry: geneBiomart
Aliases: geneBiomart
Keywords: hplot
Description: AnnotationTrack objects from biomaRt
URL: ../../../library/GenomeGraphs/html/geneBiomart.html

Entry: geneRegionBiomart
Aliases: geneRegionBiomart
Keywords: hplot
Description: Construct an AnnotationTrack object from biomaRt.
URL: ../../../library/GenomeGraphs/html/geneRegionBiomart.html

Entry: getPar
Aliases: getPar
Keywords: hplot
Description: Retrieves a display parameter from an object.
URL: ../../../library/GenomeGraphs/html/getPar.html

Entry: ideogramTab
Aliases: ideogramTab
Keywords: datasets
Description: Contains info to plot ideograms
URL: ../../../library/GenomeGraphs/html/ideogramTab.html

Entry: intensity
Aliases: intensity
Keywords: datasets
Description: Contains dummy intensity data
URL: ../../../library/GenomeGraphs/html/intensity.html

Entry: makeAnnotationTrack
Aliases: makeAnnotationTrack
Keywords: hplot
Description: Create objects of class AnnotationTrack
URL: ../../../library/GenomeGraphs/html/makeAnnotationTrack.html

Entry: makeBaseTrack
Aliases: makeBaseTrack
Keywords: hplot
Description: Creates an object of class BaseTrack
URL: ../../../library/GenomeGraphs/html/makeBaseTrack.html

Entry: makeExonArray
Aliases: makeExonArray
Keywords: hplot
Description: Creates and object of class ExonArray
URL: ../../../library/GenomeGraphs/html/makeExonArray.html

Entry: makeGene
Aliases: makeGene
Keywords: hplot
Description: Creates an object of class Gene
URL: ../../../library/GenomeGraphs/html/makeGene.html

Entry: makeGeneModel
Aliases: makeGeneModel
Keywords: hplot
Description: Creates an object of class GeneModel
URL: ../../../library/GenomeGraphs/html/makeGeneModel.html

Entry: makeGeneRegion
Aliases: makeGeneRegion
Keywords: hplot
Description: Creates an object of class Gene containing the intron-exon structures of genes
URL: ../../../library/GenomeGraphs/html/makeGeneRegion.html

Entry: makeGenericArray
Aliases: makeGenericArray
Keywords: hplot
Description: Creates an object of class GenericArray
URL: ../../../library/GenomeGraphs/html/makeGenericArray.html

Entry: makeGenomeAxis
Aliases: makeGenomeAxis
Keywords: hplot
Description: Creates an object of class GenomeAxis
URL: ../../../library/GenomeGraphs/html/makeGenomeAxis.html

Entry: makeIdeogram
Aliases: makeIdeogram
Keywords: hplot
Description: Creates object of class Ideogram
URL: ../../../library/GenomeGraphs/html/makeIdeogram.html

Entry: makeLegend
Aliases: makeLegend
Keywords: hplot
Description: Creates an object of class Legend
URL: ../../../library/GenomeGraphs/html/makeLegend.html

Entry: makeRectangleOverlay
Aliases: makeRectangleOverlay
Keywords: hplot
Description: Create a rectangular overlay
URL: ../../../library/GenomeGraphs/html/makeRectangleOverlay.html

Entry: makeSegmentation
Aliases: makeSegmentation
Keywords: hplot
Description: Create objects of class segmentation
URL: ../../../library/GenomeGraphs/html/makeSegmentation.html

Entry: makeTextOverlay
Aliases: makeTextOverlay
Keywords: hplot
Description: Create objects of class TextOverlay
URL: ../../../library/GenomeGraphs/html/makeTextOverlay.html

Entry: makeTitle
Aliases: makeTitle
Keywords: hplot
Description: Creates an object of class Title
URL: ../../../library/GenomeGraphs/html/makeTitle.html

Entry: makeTranscript
Aliases: makeTranscript
Keywords: hplot
Description: Creates an object of class Transcript
URL: ../../../library/GenomeGraphs/html/makeTranscript.html

Entry: probestart
Aliases: probestart
Keywords: datasets
Description: Contains dummy expression array probe start positions
URL: ../../../library/GenomeGraphs/html/probestart.html

Entry: segEnd
Aliases: segEnd
Keywords: datasets
Description: Contains dummy copy number segmentation end positions
URL: ../../../library/GenomeGraphs/html/segEnd.html

Entry: segStart
Aliases: segStart
Keywords: datasets
Description: Contains dummy copy number segmentation start positions data
URL: ../../../library/GenomeGraphs/html/segStart.html

Entry: segments
Aliases: segments
Keywords: datasets
Description: Contains dummy copy number segment data
URL: ../../../library/GenomeGraphs/html/segments.html

Entry: seqDataEx
Aliases: seqDataEx
Keywords: datasets
Description: This is an example data set from chromosome 4 of yeast from various publicly available datasets.
URL: ../../../library/GenomeGraphs/html/seqDataEx.html

Entry: setPar
Aliases: setPar
Keywords: hplot
Description: Sets a display parameter
URL: ../../../library/GenomeGraphs/html/setPar.html

Entry: showDisplayOptions
Aliases: showDisplayOptions
Keywords: hplot
Description: Print standard display options, DisplayPars for an object or a class
URL: ../../../library/GenomeGraphs/html/showDisplayOptions.html

Entry: unrData
Aliases: unrData
Keywords: datasets
Description: Contains exon array data
URL: ../../../library/GenomeGraphs/html/unrData.html

Entry: unrNProbes
Aliases: unrNProbes
Keywords: datasets
Description: Contains exon array data
URL: ../../../library/GenomeGraphs/html/unrNProbes.html

Entry: unrPositions
Aliases: unrPositions
Keywords: datasets
Description: Contains probe start and end positions of exon array probes
URL: ../../../library/GenomeGraphs/html/unrPositions.html

Entry: yeastCons1
Aliases: yeastCons1
Keywords: datasets
Description: Contains dummy yeast conservation data
URL: ../../../library/GenomeGraphs/html/yeastCons1.html
