Man pages for GenomeGraphs
Plotting genomic information from Ensembl
| AnnotationTrack-class | Class "AnnotationTrack" |
| BaseTrack-class | Class "BaseTrack" represents base specific data |
| cn | Contains dummy copy number data |
| DisplayPars | DisplayPars constructs objects of type DisplayPars which are... |
| DisplayPars-class | Class "DisplayPars" is used to specify graphical parameters... |
| drawGD | Generic called on each gdObject to do the plotting. |
| drawTrackOverlay-methods | This method does the drawing of a track overlay. One should... |
| ExonArray-class | Class "ExonArray" representing probe level exon array data... |
| exonProbePos | Contains dummy exon probe positions |
| gdObject-class | Class "gdObject" is the parent class of all of the objects in... |
| gdPlot | gdPlot is the main plotting function of the GenomeGraphs... |
| geneBiomart | AnnotationTrack objects from biomaRt |
| Gene-class | Class "Gene" represents the Ensembl Gene level annotation |
| GeneModel-class | Class "GeneModel", represents a custom gene model |
| geneRegionBiomart | Construct an AnnotationTrack object from biomaRt. |
| GeneRegion-class | Class "GeneRegion", representing gene structures in a defined... |
| GenericArray-class | Class "GenericArray", representing array data |
| GenomeAxis-class | Class "GenomeAxis", representing a genomic coordinate axis |
| getGenomicRange | Retrieves the genomic range of an object |
| getPar | Retrieves a display parameter from an object. |
| getSize | gets the size |
| HighlightRegion-class | Class "HighlightRegion" is used to highlight vertical blocks... |
| Ideogram-class | Class "Ideogram", represent an Ideogram |
| ideogramTab | Contains info to plot ideograms |
| ImplementsTrackOverlay-class | Class "ImplementsTrackOverlay" |
| intensity | Contains dummy intensity data |
| Legend-class | Class "Legend", represents a legend to add to a plot |
| 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... |
| 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 |
| MappedRead-class | Represents mapped reads |
| Overlay-class | Class "Overlay" |
| probestart | Contains dummy expression array probe start positions |
| RectangleOverlay-class | Class "RectangleOverlay" |
| segEnd | Contains dummy copy number segmentation end positions |
| Segmentation-class | Class "Segmentation" is used to specify segmentations to any... |
| segments | Contains dummy copy number segment data |
| segStart | Contains dummy copy number segmentation start positions data |
| seqDataEx | This is an example data set from chromosome 4 of yeast from... |
| setPar | Sets a display parameter |
| showDisplayOptions | Print standard display options, DisplayPars for an object or... |
| 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... |
| 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 |
