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,AnnotationTrack-method |
Class "AnnotationTrack" |
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,Segmentation-method |
Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack) |
drawGD,Title-method |
Class "Title" representing the title of a plot |
drawGD,Transcript-method |
Represent known transcript isoforms as annoted by Ensembl |
drawOverlay, TextOverlay-method |
Class "TextOverlay" |
drawOverlay,RectangleOverlay-method |
Class "RectangleOverlay" |
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 |
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 region |
geneRegionBiomart |
Construct an AnnotationTrack object from biomaRt. |
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. |
getPlotId,AnnotationTrack-method |
Class "AnnotationTrack" |
getPointSize,gdObject-method |
Class "gdObject" is the parent class of all of the objects in the system. |
getSegmentation,Segmentable-method |
Class "Segmentable" |
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. |
segEnd |
Contains dummy copy number segmentation end positions |
Segmentable-class |
Class "Segmentable" |
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 |
seqDataEx |
This is an example data set from chromosome 4 of yeast from various publicly available datasets. |
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 |
showDisplayOptions |
Print standard display options, DisplayPars for an object or a class |
showDisplayOptions,character-method |
Class "gdObject" is the parent class of all of the objects in the system. |
showDisplayOptions,gdObject-method |
Class "gdObject" is the parent class of all of the objects in the system. |