GWASTrack-class         Constructor for GWASTrack
display,GWASTrack-method
                        display the already constructed and configured
                        track
getUrl,GWASTrack-method
                        the url of the gwas table
get_basic_genomes       get_basic_genomes
get_cas_genomes         get_cas_genomes
get_css_genomes         get_css_genomes
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
igvShiny                Create an igvShiny instance
igvShinyOutput          create the UI for the widget
loadBamTrackFromLocalData
                        load GenomicAlignments data as an igv.js
                        alignment track
loadBamTrackFromURL     load a bam track which, with index, is served
                        up by http
loadBedGraphTrack       load a scored genome annotation track provided
                        as a data.frame
loadBedGraphTrackFromURL
                        load a bedgraph track from a URL
loadBedTrack            load a bed track provided as a data.frame
loadCramTrackFromURL    load a cram track which, with index, is served
                        up by http
loadGFF3TrackFromLocalData
                        load a GFF3 track defined by local data
loadGFF3TrackFromURL    load a GFF3 track which, with index, is served
                        up by http
loadGwasTrack           load a GWAS (genome-wide association study)
                        track provided as a data.frame
loadSegTrack            load a seg track provided as a data.frame
loadVcfTrack            load a VCF (variant) track provided as a
                        Bioconductor VariantAnnotation object
parseAndValidateGenomeSpec
                        parseAndValidateGenomeSpec
removeTracksByName      remove tracks from the browser
removeUserAddedTracks   remove only those tracks explicitly added by
                        your app
renderIgvShiny          draw the igv genome browser element
showGenomicRegion       focus igv on a region
