Man pages for Bioconductor-mirror/GenomeGraphs
Plotting genomic information from Ensembl

AnnotationTrack-classClass "AnnotationTrack"
BaseTrack-classClass "BaseTrack" represents base specific data
cnContains dummy copy number data
DisplayParsDisplayPars constructs objects of type DisplayPars which are...
DisplayPars-classClass "DisplayPars" is used to specify graphical parameters...
drawGDGeneric called on each gdObject to do the plotting.
drawTrackOverlay-methodsThis method does the drawing of a track overlay. One should...
ExonArray-classClass "ExonArray" representing probe level exon array data...
exonProbePosContains dummy exon probe positions
gdObject-classClass "gdObject" is the parent class of all of the objects in...
gdPlotgdPlot is the main plotting function of the GenomeGraphs...
geneBiomartAnnotationTrack objects from biomaRt
Gene-classClass "Gene" represents the Ensembl Gene level annotation
GeneModel-classClass "GeneModel", represents a custom gene model
geneRegionBiomartConstruct an AnnotationTrack object from biomaRt.
GeneRegion-classClass "GeneRegion", representing gene structures in a defined...
GenericArray-classClass "GenericArray", representing array data
GenomeAxis-classClass "GenomeAxis", representing a genomic coordinate axis
getGenomicRangeRetrieves the genomic range of an object
getParRetrieves a display parameter from an object.
getSizegets the size
HighlightRegion-classClass "HighlightRegion" is used to highlight vertical blocks...
Ideogram-classClass "Ideogram", represent an Ideogram
ideogramTabContains info to plot ideograms
ImplementsTrackOverlay-classClass "ImplementsTrackOverlay"
intensityContains dummy intensity data
Legend-classClass "Legend", represents a legend to add to a plot
makeAnnotationTrackCreate objects of class AnnotationTrack
makeBaseTrackCreates an object of class BaseTrack
makeExonArrayCreates and object of class ExonArray
makeGeneCreates an object of class Gene
makeGeneModelCreates an object of class GeneModel
makeGeneRegionCreates an object of class Gene containing the intron-exon...
makeGenericArrayCreates an object of class GenericArray
makeGenomeAxisCreates an object of class GenomeAxis
makeIdeogramCreates object of class Ideogram
makeLegendCreates an object of class Legend
makeRectangleOverlayCreate a rectangular overlay
makeSegmentationCreate objects of class segmentation
makeSmoothingCreate objects of class Smoothing
makeTextOverlayCreate objects of class TextOverlay
makeTitleCreates an object of class Title
makeTranscriptCreates an object of class Transcript
MappedRead-classRepresents mapped reads
Overlay-classClass "Overlay"
probestartContains dummy expression array probe start positions
RectangleOverlay-classClass "RectangleOverlay"
segEndContains dummy copy number segmentation end positions
Segmentation-classClass "Segmentation" is used to specify segmentations to any...
segmentsContains dummy copy number segment data
segStartContains dummy copy number segmentation start positions data
seqDataExThis is an example data set from chromosome 4 of yeast from...
setParSets a display parameter
showDisplayOptionsPrint standard display options, DisplayPars for an object or...
Smoothing-classClass "Smoothing"
TextOverlay-classClass "TextOverlay"
Title-classClass "Title" representing the title of a plot
TrackOverlay-classClass "TrackOverlay"
Transcript-classRepresent known transcript isoforms as annoted by Ensembl
TranscriptRegion-classClass "TranscriptRegion", representing a genomic region with...
unrDataContains exon array data
unrNProbesContains exon array data
unrPositionsContains probe start and end positions of exon array probes
yeastCons1Contains dummy yeast conservation data
Bioconductor-mirror/GenomeGraphs documentation built on May 29, 2017, 5:18 a.m.