.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 |