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| BaseTrack-class | Class "BaseTrack" represents base specific data |
| cn | Contains dummy copy number 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. |
| drawGD | Generic called on each gdObject to do the plotting. |
| drawGD,BaseTrack-method | Class "BaseTrack" represents base specific data |
| drawGD,ExonArray-method | Class "ExonArray" representing probe level exon array data from Affymetrix |
| drawGD,Gene-method | Class "Gene" represents the Ensembl Gene level annotation |
| drawGD,GeneModel-method | Class "GeneModel", represents a custom gene model |
| drawGD,GeneRegion-method | Class "GeneRegion", representing gene structures in a defined genomic region |
| drawGD,GenericArray-method | Class "GenericArray", representing array data |
| drawGD,GenomeAxis-method | Class "GenomeAxis", representing a genomic coordinate axis |
| drawGD,Ideogram-method | Class "Ideogram", represent an Ideogram |
| drawGD,Legend-method | Class "Legend", represents a legend to add to a plot |
| drawGD,MappedRead-method | Represents mapped reads |
| drawGD,Title-method | Class "Title" representing the title of a plot |
| drawGD,Transcript-method | Represent known transcript isoforms as annoted by Ensembl |
| ExonArray-class | Class "ExonArray" representing probe level exon array data from Affymetrix |
| 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 |
| 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 |
| getCex,gdObject-method | Class "gdObject" is the parent class of all of the objects in the system. |
| getColor,gdObject-method | Class "gdObject" is the parent class of all of the objects in the system. |
| getLty,gdObject-method | Class "gdObject" is the parent class of all of the objects in the system. |
| getLwd,gdObject-method | Class "gdObject" is the parent class of all of the objects in the system. |
| getPar | Retrieves a display parameter from an object. |
| getPar,DisplayPars-method | Class "DisplayPars" is used to specify graphical parameters to gdObjects. |
| getPar,gdObject-method | Class "gdObject" is the parent class of all of the objects in the system. |
| getPch,gdObject-method | Class "gdObject" is the parent class of all of the objects in the system. |
| getPointSize,gdObject-method | Class "gdObject" is the parent class of all of the objects in the system. |
| getSegmentEnd,Segmentation-method | Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack) |
| getSegments,Segmentation-method | Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack) |
| getSegmentStart,Segmentation-method | Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack) |
| getSize,gdObject-method | Class "gdObject" is the parent class of all of the objects in the system. |
| HighlightRegion-class | Class "HighlightRegion" is used to highlight vertical blocks of genomic regions. |
| Ideogram-class | Class "Ideogram", represent an Ideogram |
| ideogramTab | Contains info to plot ideograms |
| initialize,DisplayPars-method | Class "DisplayPars" is used to specify graphical parameters to gdObjects. |
| initialize,gdObject-method | Class "gdObject" is the parent class of all of the objects in the system. |
| initialize,Gene-method | Class "Gene" represents the Ensembl Gene level annotation |
| initialize,GeneRegion-method | Class "GeneRegion", representing gene structures in a defined genomic region |
| initialize,Transcript-method | Represent known transcript isoforms as annoted by Ensembl |
| intensity | Contains dummy intensity data |
| Legend-class | Class "Legend", represents a legend to add to a plot |
| MappedRead-class | Represents mapped reads |
| probestart | Contains dummy expression array probe start positions |
| segEnd | Contains dummy copy number segmentation end positions |
| Segmentation-class | Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack) |
| segments | Contains dummy copy number segment data |
| segStart | Contains dummy copy number segmentation start positions data |
| setPar | Sets a display parameter |
| setPar,DisplayPars-method | Class "DisplayPars" is used to specify graphical parameters to gdObjects. |
| setPar,gdObject-method | Class "gdObject" is the parent class of all of the objects in the system. |
| show,BaseTrack-method | Class "BaseTrack" represents base specific data |
| show,DisplayPars-method | Class "DisplayPars" is used to specify graphical parameters to gdObjects. |
| show,ExonArray-method | Class "ExonArray" representing probe level exon array data from Affymetrix |
| show,Gene-method | Class "Gene" represents the Ensembl Gene level annotation |
| show,GeneRegion-method | Class "GeneRegion", representing gene structures in a defined genomic region |
| show,GenericArray-method | Class "GenericArray", representing array data |
| show,MappedRead-method | Represents mapped reads |
| show,Transcript-method | Represent known transcript isoforms as annoted by Ensembl |
| show,TranscriptRegion-method | Class "TranscriptRegion", representing a genomic region with transcripts |
| Title-class | Class "Title" representing the title of a plot |
| Transcript-class | Represent known transcript isoforms as annoted by Ensembl |
| TranscriptRegion-class | Class "TranscriptRegion", representing a genomic region with transcripts |
| 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 |