igvR: integrative genomics viewer


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Documentation for package ‘igvR’ version 1.22.0

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.BedpeInteractionsTrack Constructor for BedpeInteractionsTrack
.DataFrameAnnotationTrack Constructor for DataFrameAnnotationTrack
.DataFrameQuantitativeTrack Constructor for DataFrameQuantitativeTrack
.GenomicAlignmentTrack Constructor for GenomicAlignmentTrack
.GFF3Track Constructor for GFF3Track
.GRangesAnnotationTrack Constructor for GRangesAnnotationTrack
.GRangesQuantitativeTrack Constructor for GRangesQuantitativeTrack
.GWASTrack Constructor for GWASTrack
.GWASUrlTrack Constructor for GWASTrack
.igvAnnotationTrack Constructor for igvAnnotationTrack
.igvR Create an igvR object
.QuantitativeTrack Constructor for QuantitativeTrack
.RemoteAlignmentTrack Constructor for RemoteAlignmentTrack
.Track Constructor for Track
.UCSCBedAnnotationTrack Constructor for UCSCBedAnnotationTrack
.UCSCBedGraphQuantitativeTrack Constructor for UCSCBedGraphQuantitativeTrack
BedpeInteractionsTrack Constructor for BedpeInteractionsTrack
BedpeInteractionsTrack-class Constructor for BedpeInteractionsTrack
currently.supported.stock.genomes currently.supported.stock.genomes
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
enableMotifLogoPopups turn mottif log popups on or off
enableMotifLogoPopups-method turn mottif log popups on or off
GenomicAlignmentTrack Constructor for GenomicAlignmentTrack
GenomicAlignmentTrack-class Constructor for GenomicAlignmentTrack
getGenomicRegion Obtain the chromosome and coordiates of the currently displayed genomic region.
getGenomicRegion-method Obtain the chromosome and coordiates of the currently displayed genomic region.
getSupportedGenomes Get the shorthand codes (eg, "hg38") for the genomes currently supported by our use of igv.js
getSupportedGenomes-method Get the shorthand codes (eg, "hg38") for the genomes currently supported by our use of igv.js
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
GFF3Track Constructor for GFF3Track
GFF3Track-class Constructor for GFF3Track
GRangesAnnotationTrack Constructor for GRangesAnnotationTrack
GRangesAnnotationTrack-class Constructor for GRangesAnnotationTrack
GRangesQuantitativeTrack Constructor for GRangesQuantitativeTrack
GRangesQuantitativeTrack-class Constructor for GRangesQuantitativeTrack
GWASTrack Constructor for GWASTrack
GWASTrack-class Constructor for GWASTrack
GWASUrlTrack Constructor for GWASUrlTrack
igvAnnotationTrack Constructor for igvAnnotationTrack
igvAnnotationTrack-class Constructor for igvAnnotationTrack
igvR Create an igvR object
igvR-class Create an igvR object
parseAndValidateGenomeSpec parseAndValidateGenomeSpec
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
RemoteAlignmentTrack Constructor for RemoteAlignmentTrack
RemoteAlignmentTrack-class Constructor for RemoteAlignmentTrack
removeTracksByName Remove named tracks
removeTracksByName-method Remove named tracks
saveToSVG Get entire igv browser image in svg
saveToSVG-method Get entire igv browser image in svg
setCustomGenome Specify the reference genome you wish to use, via full specification of all urls
setCustomGenome-method Specify the reference genome you wish to use, via full specification of all urls
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.
setTrackClickFunction Specify (supply) the javascript function run on track click event
setTrackClickFunction-method Specify (supply) the javascript function run on track click event
setTrackHeight Remove named tracks
setTrackHeight-method Remove named tracks
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
showTrackLabels Hide or show igv track labels
showTrackLabels-method Hide or show igv track labels
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 BedpeInteractionsTrack
trackSize-method Retrieve the size of the DataFrameAnnotationTrack
trackSize-method Retrieve the size of the DataFrameQuantitativeTrack
trackSize-method Retrieve the size of the GFF3Track
trackSize-method Retrieve the size of the GRangesAnnotationTrack
trackSize-method Retrieve the size of the GRangesQuantitativeTrack
trackSize-method Retrieve the size of the GWASTrack
trackSize-method Retrieve the size of the GWASUrlTrack
trackSize-method Retrieve the size of the GenomicAlignmentTrack
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
url.exists url.exists
VariantTrack Constructor for VariantTrack
VariantTrack-class Constructor for VariantTrack
zoomIn zoom the genome view in by a factor of 2
zoomIn-method zoom the genome view in by a factor of 2
zoomOut zoom the genome view out by a factor of 2
zoomOut-method zoom the genome view out by a factor of 2