| .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 |
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