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

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.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