Man pages for paul-shannon/igvR
igvR: integrative genomics viewer
| BedpeInteractionsTrack-class | Constructor for BedpeInteractionsTrack |
| currently.supported.stock.genomes | currently.supported.stock.genomes |
| DataFrameAnnotationTrack-class | Constructor for DataFrameAnnotationTrack |
| DataFrameQuantitativeTrack-class | Constructor for DataFrameQuantitativeTrack |
| displayTrack | display the specified track in igv |
| enableMotifLogoPopups | turn mottif log popups on or off |
| GenomicAlignmentTrack-class | Constructor for GenomicAlignmentTrack |
| getGenomicRegion | Obtain the chromosome and coordiates of the currently... |
| getSupportedGenomes | Get the shorthand codes (eg, "hg38") for the genomes... |
| getTrackNames | Get the names of all the tracks currently displayed in igv |
| GFF3Track-class | Constructor for GFF3Track |
| GRangesAnnotationTrack-class | Constructor for GRangesAnnotationTrack |
| GRangesQuantitativeTrack-class | Constructor for GRangesQuantitativeTrack |
| GWASTrack-class | Constructor for GWASTrack |
| GWASUrlTrack-class | Constructor for GWASUrlTrack |
| igvAnnotationTrack-class | Constructor for igvAnnotationTrack |
| igvR-class | Create an igvR object |
| parseAndValidateGenomeSpec | parseAndValidateGenomeSpec |
| ping | Test the connection between your R session and the webapp |
| QuantitativeTrack-class | Constructor for QuantitativeTrack |
| RemoteAlignmentTrack-class | Constructor for RemoteAlignmentTrack |
| removeTracksByName | Remove named tracks |
| saveToSVG | Get entire igv browser image in svg |
| setCustomGenome | Specify the reference genome you wish to use, via full... |
| setGenome | Specify the reference genome, currently limited to hg38,... |
| setTrackClickFunction | Specify (supply) the javascript function run on track click... |
| setTrackHeight | Remove named tracks |
| showGenomicRegion | Set the visible region, by explicit chromLoc string, or by... |
| showTrackLabels | Hide or show igv track labels |
| Track-class | Constructor for Track |
| trackInfo | Get basic info about a track: its type, file format, source... |
| trackSize | Retrieve the size of the QuantitativeTrack |
| trackSize-BedpeInteractionsTrack-method | Retrieve the size of the BedpeInteractionsTrack |
| trackSize-DataFrameAnnotationTrack-method | Retrieve the size of the DataFrameAnnotationTrack |
| trackSize-DataFrameQuantitativeTrack-method | Retrieve the size of the DataFrameQuantitativeTrack |
| trackSize-GenomicAlignmentTrack-method | Retrieve the size of the GenomicAlignmentTrack |
| trackSize-GFF3Track-method | Retrieve the size of the GFF3Track |
| trackSize-GRangesAnnotationTrack-method | Retrieve the size of the GRangesAnnotationTrack |
| trackSize-GRangesQuantitativeTrack-method | Retrieve the size of the GRangesQuantitativeTrack |
| trackSize-GWASTrack-method | Retrieve the size of the GWASTrack |
| trackSize-GWASUrlTrack-method | Retrieve the size of the GWASUrlTrack |
| trackSize-UCSCBedAnnotationTrack-method | Retrieve the size of theUCSCBedAnnotationTrack |
| trackSize-UCSCBedGraphQuantitativeTrack-method | Retrieve the size of the UCSCBedGraphQuantitativeTrack |
| trackSize-VariantTrack-method | Retrieve the size of the VariantTrack |
| UCSCBedAnnotationTrack-class | Constructor for UCSCBedAnnotationTrack |
| UCSCBedGraphQuantitativeTrack-class | Constructor for UCSCBedGraphQuantitativeTrack |
| url.exists | url.exists |
| VariantTrack-class | Constructor for VariantTrack |
| zoomIn | zoom the genome view in by a factor of 2 |
| zoomOut | zoom the genome view out by a factor of 2 |
