Last data update: 2014.03.03

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AnnotationTrack-class (Package: GenomeGraphs) : Class "AnnotationTrack"

A generic object to store annotation
● Data Source: BioConductor
● Keywords: classes
● Alias: AnnotationTrack-class, drawGD,AnnotationTrack-method, getPlotId,AnnotationTrack-method, initialize,AnnotationTrack-method
● 0 images

BaseTrack-class (Package: GenomeGraphs) : Class "BaseTrack" represents base specific data

Represents specific data, e.g. how many times was every base sequenced
● Data Source: BioConductor
● Keywords: classes
● Alias: BaseTrack-class, drawGD,BaseTrack-method, show,BaseTrack-method
1 images

DisplayPars-class (Package: GenomeGraphs) : Class "DisplayPars" is used to specify graphical parameters to

The DisplayPars functions analagously to par and gp. Generally the class is instantiated using the DisplayPars function rather than directly.
● Data Source: BioConductor
● Keywords: classes
● Alias: DisplayPars-class, getPar,DisplayPars-method, initialize,DisplayPars-method, setPar,DisplayPars-method, show,DisplayPars-method
2 images

DisplayPars (Package: GenomeGraphs) : DisplayPars constructs objects of type DisplayPars which are used

DisplayPars takes any number of named arguments which will be used by the drawGD method of the gdObject. These arguments are analagous to both par and gp of the traditional and grid graphics systems respectively. Different functions support different graphical parameters - thus it is necessary to consult the documentation of the particular gdObject to determine which DisplayPars will be used.
● Data Source: BioConductor
● Keywords: hplot
● Alias: DisplayPars
1 images

ExonArray-class (Package: GenomeGraphs) : Class "ExonArray" representing probe level exon array data from Affymetrix

Represents probe level exon array data from Affymetrix. Makes it possible to visualize alternative splicing as measured by the Affymetrix exon array platform and relate it to known transcript isoforms annotated by Ensembl
● Data Source: BioConductor
● Keywords: classes
● Alias: ExonArray-class, drawGD,ExonArray-method, show,ExonArray-method
1 images

Gene-class (Package: GenomeGraphs) : Class "Gene" represents the Ensembl Gene level annotation

Class "Gene" represents the Ensembl Gene level annotation. Upon creation of an object of this class, intron and exon boundaries are retrieved from Ensembl
● Data Source: BioConductor
● Keywords: classes
● Alias: Gene-class, drawGD,Gene-method, initialize,Gene-method, show,Gene-method
1 images

GeneModel-class (Package: GenomeGraphs) : Class "GeneModel", represents a custom gene model

This class represents a custom gene model defined by exon boundaries. An example of this class could be an Affymetrix gene model used to create the Affy Exon array
● Data Source: BioConductor
● Keywords: classes
● Alias: GeneModel-class, drawGD,GeneModel-method
1 images

GeneRegion-class (Package: GenomeGraphs) : Class "GeneRegion", representing gene structures in a defined genomic region

Given a start and end position and a chromosome name, all gene structures in this region will be retrieved from Ensembl upon creation of the object.
● Data Source: BioConductor
● Keywords: classes
● Alias: GeneRegion-class, drawGD,GeneRegion-method, initialize,GeneRegion-method, show,GeneRegion-method
1 images

GenericArray-class (Package: GenomeGraphs) : Class "GenericArray", representing array data

The Generic Array class is a class that can be used to create plots from array data such as microarrays and arrayCGH platforms. It can represent, the data as line plots or dot plots and segments can be included as well
● Data Source: BioConductor
● Keywords: classes
● Alias: GenericArray-class, drawGD,GenericArray-method, show,GenericArray-method
1 images

GenomeAxis-class (Package: GenomeGraphs) : Class "GenomeAxis", representing a genomic coordinate axis

Represents a genomic coordinate axis
● Data Source: BioConductor
● Keywords: classes
● Alias: GenomeAxis-class, drawGD,GenomeAxis-method
1 images