Function reference
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igvShiny() - Create an igvShiny instance
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igvShinyOutput() - create the UI for the widget
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parseAndValidateGenomeSpec() - parseAndValidateGenomeSpec
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removeTracksByName() - remove tracks from the browser
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removeUserAddedTracks() - remove only those tracks explicitly added by your app
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renderIgvShiny() - draw the igv genome browser element
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showGenomicRegion()getGenomicRegion() - focus igv on a region
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loadBamTrackFromLocalData() - load GenomicAlignments data as an igv.js alignment track
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loadBamTrackFromURL() - load a bam track which, with index, is served up by http
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loadBedGraphTrackFromURL() - load a bedgraph track from a URL
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loadBedTrack() - load a bed track provided as a data.frame
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loadCramTrackFromURL() - load a cram track which, with index, is served up by http
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loadGFF3TrackFromLocalData() - load a GFF3 track defined by local data
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loadGFF3TrackFromURL() - load a GFF3 track which, with index, is served up by http
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loadBedGraphTrack() - load a scored genome annotation track provided as a data.frame
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loadGwasTrack() - load a GWAS (genome-wide association study) track provided as a data.frame
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loadSegTrack() - load a seg track provided as a data.frame
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loadVcfTrack() - load a VCF (variant) track provided as a Bioconductor VariantAnnotation object
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GWASTrack() - Constructor for GWASTrack
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display(<GWASTrack>) - display the already constructed and configured track
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getUrl(<GWASTrack>) - the url of the gwas table
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get_basic_genomes() - get_basic_genomes
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get_cas_genomes() - get_cas_genomes
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get_css_genomes() - get_css_genomes
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get_tracks_dir() - get_tracks_dir Get the directory where tracks are stored. The directory can be defined with environmental variable. If not defined the default is a directory called "tracks" in the temp directory. We need a local directory to write files - for instance, a vcf file representing a genomic region of interest. We then tell shiny about that directory, so that shiny's built-in http server can serve up files we write there, ultimately consumed by igv.js