Plotting genomic information from Ensembl

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Documentation for package ‘GenomeGraphs’ version 1.30.0

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A B C D E G H I L M O P R S T U Y

-- A --

AnnotationTrack-class Class "AnnotationTrack"

-- B --

BaseTrack-class Class "BaseTrack" represents base specific data

-- C --

cn Contains dummy copy number data

-- D --

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-method Class "AnnotationTrack"
drawGD-method Class "BaseTrack" represents base specific data
drawGD-method Class "ExonArray" representing probe level exon array data from Affymetrix
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 region
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 extends Segmentable (GenericArray, BaseTrack)
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 this method to gain track plotting functionality.
drawTrackOverlay-methods This method does the drawing of a track overlay. One should implement this method to gain track plotting functionality.

-- E --

ExonArray-class Class "ExonArray" representing probe level exon array data from Affymetrix
exonProbePos Contains dummy exon probe positions

-- G --

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-method Class "gdObject" is the parent class of all of the objects in the system.
getColor-method Class "gdObject" is the parent class of all of the objects in the system.
getGenomicRange Retrieves the genomic range of an object
getGenomicRange-method Retrieves the genomic range of an object
getLty-method Class "gdObject" is the parent class of all of the objects in the system.
getLwd-method Class "gdObject" is the parent class of all of the objects in the system.
getPar Retrieves a display parameter from an object.
getPar-method Class "DisplayPars" is used to specify graphical parameters to gdObjects.
getPar-method Class "gdObject" is the parent class of all of the objects in the system.
getPch-method Class "gdObject" is the parent class of all of the objects in the system.
getPlotId-method Class "AnnotationTrack"
getPointSize-method Class "gdObject" is the parent class of all of the objects in the system.
getSegmentEnd-method Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack)
getSegments-method Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack)
getSegmentStart-method Class "Segmentation" is used to specify segmentations to any class that extends Segmentable (GenericArray, BaseTrack)
getSize gets the size
getSize-method Class "gdObject" is the parent class of all of the objects in the system.

-- H --

HighlightRegion-class Class "HighlightRegion" is used to highlight vertical blocks of genomic regions.

-- I --

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 gdObjects.
initialize-method Class "Gene" represents the Ensembl Gene level annotation
initialize-method Class "GeneRegion", representing gene structures in a defined genomic region
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 system.
intensity Contains dummy intensity data

-- L --

Legend-class Class "Legend", represents a legend to add to a plot

-- M --

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 of genes
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

-- O --

Overlay-class Class "Overlay"

-- P --

probestart Contains dummy expression array probe start positions

-- R --

RectangleOverlay-class Class "RectangleOverlay"

-- S --

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
seqDataEx This is an example data set from chromosome 4 of yeast from various publicly available datasets.
setPar Sets a display parameter
setPar-method Class "DisplayPars" is used to specify graphical parameters to gdObjects.
setPar-method Class "gdObject" is the parent class of all of the objects in the system.
show-method Class "BaseTrack" represents base specific data
show-method Class "DisplayPars" is used to specify graphical parameters to gdObjects.
show-method Class "ExonArray" representing probe level exon array data from Affymetrix
show-method Class "Gene" represents the Ensembl Gene level annotation
show-method Class "GeneRegion", representing gene structures in a defined genomic region
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 transcripts
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 system.
Smoothing-class Class "Smoothing"

-- T --

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 transcripts

-- U --

unrData Contains exon array data
unrNProbes Contains exon array data
unrPositions Contains probe start and end positions of exon array probes

-- Y --

yeastCons1 Contains dummy yeast conservation data