A B C D E G H I L M O P R S T U Y
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 used to |
DisplayPars-class | Class "DisplayPars" is used to specify graphical parameters to |
drawGD | Generic called on each gdObject to do the plotting. |
drawGD-method | Class "AnnotationTrack" |
drawGD-method | Class "BaseTrack" represents base specific data |
drawGD-method | Class "ExonArray" representing probe level exon array data from |
drawGD-method | Class "Gene" represents the Ensembl Gene level annotation |
drawGD-method | Class "GeneModel", represents a custom gene model |
drawGD-method | Class "GeneRegion", representing gene structures in a defined genomic |
drawGD-method | Class "GenericArray", representing array data |
drawGD-method | Class "GenomeAxis", representing a genomic coordinate axis |
drawGD-method | Class "Ideogram", represent an Ideogram |
drawGD-method | Class "Legend", represents a legend to add to a plot |
drawGD-method | Represents mapped reads |
drawGD-method | Class "Segmentation" is used to specify segmentations to any class that |
drawGD-method | Class "Title" representing the title of a plot |
drawGD-method | Represent known transcript isoforms as annoted by Ensembl |
drawOverlay-method | Class "RectangleOverlay" |
drawOverlay-method | Class "TextOverlay" |
drawTrackOverlay-method | This method does the drawing of a track overlay. One should implement |
drawTrackOverlay-methods | This method does the drawing of a track overlay. One should implement |
ExonArray-class | Class "ExonArray" representing probe level exon array data from |
exonProbePos | Contains dummy exon probe positions |
gdObject-class | Class "gdObject" is the parent class of all of the objects in the |
gdPlot | gdPlot is the main plotting function of the GenomeGraphs package |
Gene-class | Class "Gene" represents the Ensembl Gene level annotation |
geneBiomart | AnnotationTrack objects from biomaRt |
GeneModel-class | Class "GeneModel", represents a custom gene model |
GeneRegion-class | Class "GeneRegion", representing gene structures in a defined genomic |
geneRegionBiomart | Construct an AnnotationTrack object from biomaRt. |
GenericArray-class | Class "GenericArray", representing array data |
GenomeAxis-class | Class "GenomeAxis", representing a genomic coordinate axis |
getCex-method | Class "gdObject" is the parent class of all of the objects in the |
getColor-method | Class "gdObject" is the parent class of all of the objects in the |
getLty-method | Class "gdObject" is the parent class of all of the objects in the |
getLwd-method | Class "gdObject" is the parent class of all of the objects in the |
getPar | Retrieves a display parameter from an object. |
getPar-method | Class "DisplayPars" is used to specify graphical parameters to |
getPar-method | Class "gdObject" is the parent class of all of the objects in the |
getPch-method | Class "gdObject" is the parent class of all of the objects in the |
getPlotId-method | Class "AnnotationTrack" |
getPointSize-method | Class "gdObject" is the parent class of all of the objects in the |
getSegmentEnd-method | Class "Segmentation" is used to specify segmentations to any class that |
getSegments-method | Class "Segmentation" is used to specify segmentations to any class that |
getSegmentStart-method | Class "Segmentation" is used to specify segmentations to any class that |
getSize-method | Class "gdObject" is the parent class of all of the objects in the |
HighlightRegion-class | Class "HighlightRegion" is used to highlight vertical blocks of genomic |
Ideogram-class | Class "Ideogram", represent an Ideogram |
ideogramTab | Contains info to plot ideograms |
ImplementsTrackOverlay-class | Class "ImplementsTrackOverlay" |
initialize-method | Class "AnnotationTrack" |
initialize-method | Class "DisplayPars" is used to specify graphical parameters to |
initialize-method | Class "Gene" represents the Ensembl Gene level annotation |
initialize-method | Class "GeneRegion", representing gene structures in a defined genomic |
initialize-method | Represent known transcript isoforms as annoted by Ensembl |
initialize-method | Class "gdObject" is the parent class of all of the objects in the |
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 structures |
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 class that |
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 various |
setPar | Sets a display parameter |
setPar-method | Class "DisplayPars" is used to specify graphical parameters to |
setPar-method | Class "gdObject" is the parent class of all of the objects in the |
show-method | Class "BaseTrack" represents base specific data |
show-method | Class "DisplayPars" is used to specify graphical parameters to |
show-method | Class "ExonArray" representing probe level exon array data from |
show-method | Class "Gene" represents the Ensembl Gene level annotation |
show-method | Class "GeneRegion", representing gene structures in a defined genomic |
show-method | Class "GenericArray", representing array data |
show-method | Represents mapped reads |
show-method | Represent known transcript isoforms as annoted by Ensembl |
show-method | Class "TranscriptRegion", representing a genomic region with |
showDisplayOptions | Print standard display options, DisplayPars for an object or a class |
showDisplayOptions-method | Class "gdObject" is the parent class of all of the objects in the |
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 |