igvR: integrative genomics viewer


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Documentation for package ‘igvR’ version 1.0.1

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.AnnotationTrack Constructor for AnnotationTrack
.DataFrameAnnotationTrack Constructor for DataFrameAnnotationTrack
.DataFrameQuantitativeTrack Constructor for DataFrameQuantitativeTrack
.GRangesAnnotationTrack Constructor for GRangesAnnotationTrack
.GRangesQuantitativeTrack Constructor for GRangesQuantitativeTrack
.igvR Create an igvR object
.QuantitativeTrack Constructor for QuantitativeTrack
.Track Constructor for Track
.UCSCBedAnnotationTrack Constructor for UCSCBedAnnotationTrack
.UCSCBedGraphQuantitativeTrack Constructor for UCSCBedGraphQuantitativeTrack
AnnotationTrack Constructor for AnnotationTrack
AnnotationTrack-class Constructor for AnnotationTrack
DataFrameAnnotationTrack Constructor for DataFrameAnnotationTrack
DataFrameAnnotationTrack-class Constructor for DataFrameAnnotationTrack
DataFrameQuantitativeTrack Constructor for DataFrameQuantitativeTrack
DataFrameQuantitativeTrack-class Constructor for DataFrameQuantitativeTrack
displayTrack display the specified track in igv
displayTrack-method display the specified track in igv
getGenomicRegion Obtain the chromosome and coordiates of the currently display genomic region.
getGenomicRegion-method Obtain the chromosome and coordiates of the currently display genomic region.
getTrackNames Get the names of all the tracks currently displayed in igv
getTrackNames-method Get the names of all the tracks currently displayed in igv
GRangesAnnotationTrack Constructor for GRangesAnnotationTrack
GRangesAnnotationTrack-class Constructor for GRangesAnnotationTrack
GRangesQuantitativeTrack Constructor for GRangesQuantitativeTrack
GRangesQuantitativeTrack-class Constructor for GRangesQuantitativeTrack
igvR Create an igvR object
igvR-class Create an igvR object
ping Test the connection between your R session and the webapp
ping-method Test the connection between your R session and the webapp
QuantitativeTrack Constructor for QuantitativeTrack
QuantitativeTrack-class Constructor for QuantitativeTrack
removeTracksByName Remove named tracks
removeTracksByName-method Remove named tracks
setGenome Specify the reference genome, currently limited to hg38, hg19, mm10, tair10.
setGenome-method Specify the reference genome, currently limited to hg38, hg19, mm10, tair10.
showGenomicRegion Set the visible region, by explicit chromLoc string, or by named features in any curently loaded annotation tracks
showGenomicRegion-method Set the visible region, by explicit chromLoc string, or by named features in any curently loaded annotation tracks
Track Constructor for Track
Track-class Constructor for Track
trackInfo Get basic info about a track: its type, file format, source and S4 class name
trackInfo-method Get basic info about a track: its type, file format, source and S4 class name
trackSize Retrieve the size of the QuantitativeTrack
trackSize-method Retrieve the size of the DataFrameAnnotationTrack
trackSize-method Retrieve the size of the DataFrameQuantitativeTrack
trackSize-method Retrieve the size of the GRangesAnnotationTrack
trackSize-method Retrieve the size of the GRangesQuantitativeTrack
trackSize-method Retrieve the size of theUCSCBedAnnotationTrack
trackSize-method Retrieve the size of the UCSCBedGraphQuantitativeTrack
trackSize-method Retrieve the size of the VariantTrack
trackSize-method Retrieve the size of the QuantitativeTrack
UCSCBedAnnotationTrack Constructor for UCSCBedAnnotationTrack
UCSCBedAnnotationTrack-class Constructor for UCSCBedAnnotationTrack
UCSCBedGraphQuantitativeTrack Constructor for UCSCBedGraphQuantitativeTrack
UCSCBedGraphQuantitativeTrack-class Constructor for UCSCBedGraphQuantitativeTrack
VariantTrack Constructor for VariantTrack
VariantTrack-class Constructor for VariantTrack