# igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)

## Documentation for package ‘igvShiny’ version 1.9.6

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

.GWASTrack | Constructor for GWASTrack
.sanitizeAndMergeOptions | Sanitize and merge track configuration options
.sanitizeTracks | Sanitize a list of startup track specifications
display | display the already constructed and configured track
display-method | display the already constructed and configured track
getGenomicRegion | focus igv on a region
getUrl | the url of the gwas table
getUrl-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
GWASTrack | Constructor for GWASTrack
GWASTrack-class | Constructor for GWASTrack
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
loadGenomeAnnotationTrack | load a scored genome annotation track provided as a data.frame
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
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