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

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Documentation for package ‘igvShiny’ version 1.9.42

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

Help Pages

.GWASTrack	Constructor for GWASTrack
.packJunctionAttributes	Pack junction attributes into a bed name column
.sanitizeAndMergeOptions	Sanitize and merge track configuration options
.sanitizeChromosomeColorMap	Check a chromosome color map before it reaches igv.js
.sanitizeTrack	Sanitize one startup track specification
.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
loadCramTrackFromLocalData	load a cram file sitting on the same machine as the shiny app
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
loadSpliceJunctionTrackFromLocalData	load a splice junction track from a data.frame
loadSpliceJunctionTrackFromURL	load a splice junction track served up by http
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
show-method	Display a short summary of a GWASTrack object
showGenomicRegion	focus igv on a region