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 1.0.0

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

Help Pages

.GWASTrack	Constructor for GWASTrack
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