Plotting genomic information from Ensembl


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Documentation for package ‘GenomeGraphs’ version 1.0.1

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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