# igvR: integrative genomics viewer

## Documentation for package ‘igvR’ version 1.33.2

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

## Help Pages

B C D E G I P Q R S T U V Z misc

## -- B --

BedpeInteractionsTrack | Constructor for BedpeInteractionsTrack
BedpeInteractionsTrack-class | Constructor for BedpeInteractionsTrack

## -- C --

CramTrack | Constructor for CramTrack
CramTrack-class | Constructor for CramTrack
currently.supported.stock.genomes | currently.supported.stock.genomes

## -- D --

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

## -- E --

enableMotifLogoPopups | turn mottif log popups on or off
enableMotifLogoPopups-method | turn mottif log popups on or off

## -- G --

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

## -- I --

igvAnnotationTrack | Constructor for igvAnnotationTrack
igvAnnotationTrack-class | Constructor for igvAnnotationTrack
igvR | Create an igvR object
igvR-class | Create an igvR object

## -- P --

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

## -- Q --

QuantitativeTrack | Constructor for QuantitativeTrack
QuantitativeTrack-class | Constructor for QuantitativeTrack

## -- R --

RemoteAlignmentTrack | Constructor for RemoteAlignmentTrack
RemoteAlignmentTrack-class | Constructor for RemoteAlignmentTrack
removeTracksByName | Remove named tracks
removeTracksByName-method | Remove named tracks

## -- S --

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

## -- T --

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

## -- U --

UCSCBedAnnotationTrack | Constructor for UCSCBedAnnotationTrack
UCSCBedAnnotationTrack-class | Constructor for UCSCBedAnnotationTrack
UCSCBedGraphQuantitativeTrack | Constructor for UCSCBedGraphQuantitativeTrack
UCSCBedGraphQuantitativeTrack-class | Constructor for UCSCBedGraphQuantitativeTrack
url.exists | url.exists

## -- V --

VariantTrack | Constructor for VariantTrack
VariantTrack-class | Constructor for VariantTrack

## -- Z --

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

## -- misc --

.BedpeInteractionsTrack | Constructor for BedpeInteractionsTrack
.CramTrack | Constructor for CramTrack
.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