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| .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 |