.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 |