# igvR: integrative genomics viewer

## Documentation for package ‘igvR’ version 1.6.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.DataFrameAnnotationTrack | Constructor for DataFrameAnnotationTrack
.DataFrameQuantitativeTrack | Constructor for DataFrameQuantitativeTrack
.GenomicAlignmentTrack | Constructor for GenomicAlignmentTrack
.GRangesAnnotationTrack | Constructor for GRangesAnnotationTrack
.GRangesQuantitativeTrack | Constructor for GRangesQuantitativeTrack
.igvAnnotationTrack | Constructor for igvAnnotationTrack
.igvR | Create an igvR object
.QuantitativeTrack | Constructor for QuantitativeTrack
.Track | Constructor for Track
.UCSCBedAnnotationTrack | Constructor for UCSCBedAnnotationTrack
.UCSCBedGraphQuantitativeTrack | Constructor for UCSCBedGraphQuantitativeTrack
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
GRangesAnnotationTrack | Constructor for GRangesAnnotationTrack
GRangesAnnotationTrack-class | Constructor for GRangesAnnotationTrack
GRangesQuantitativeTrack | Constructor for GRangesQuantitativeTrack
GRangesQuantitativeTrack-class | Constructor for GRangesQuantitativeTrack
igvAnnotationTrack | Constructor for igvAnnotationTrack
igvAnnotationTrack-class | Constructor for igvAnnotationTrack
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
saveToSVG | Get entire igv browser image in svg
saveToSVG-method | Get entire igv browser image in svg
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 | Set the visible region, by explicit chromLoc string, or by named features in any curently loaded annotation tracks
setTrackClickFunction-method | Set the visible region, by explicit chromLoc string, or by named features in any curently loaded annotation 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
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 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
VariantTrack | Constructor for VariantTrack
VariantTrack-class | Constructor for VariantTrack