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 1.9.52

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.BedpeInteractionsTrack BedpeInteractionsTrack: paired-end interactions from a bedpe data.frame
.CramTrack Alignment tracks: in-memory reads, a bam url or a cram url
.DataFrameAnnotationTrack Annotation tracks: bed-like features from a data.frame, GRanges or UCSCData
.DataFrameQuantitativeTrack Quantitative tracks: scored intervals from a data.frame, GRanges or UCSCData
.GenomicAlignmentTrack Alignment tracks: in-memory reads, a bam url or a cram url
.GFF3Track GFF3Track: gene models from a GFF3 data.frame or url
.GRangesAnnotationTrack Annotation tracks: bed-like features from a data.frame, GRanges or UCSCData
.GRangesQuantitativeTrack Quantitative tracks: scored intervals from a data.frame, GRanges or UCSCData
.GWASTrack Constructor for GWASTrack
.igvAnnotationTrack Annotation tracks: bed-like features from a data.frame, GRanges or UCSCData
.packJunctionAttributes Pack junction attributes into a bed name column
.QuantitativeTrack Quantitative tracks: scored intervals from a data.frame, GRanges or UCSCData
.RemoteAlignmentTrack Alignment tracks: in-memory reads, a bam url or a cram url
.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
.Track Track: the base class of igvShiny's S4 tracks
.UCSCBedAnnotationTrack Annotation tracks: bed-like features from a data.frame, GRanges or UCSCData
.UCSCBedGraphQuantitativeTrack Quantitative tracks: scored intervals from a data.frame, GRanges or UCSCData
.VariantTrack VariantTrack: variants from a VariantAnnotation VCF object
BedpeInteractionsTrack BedpeInteractionsTrack: paired-end interactions from a bedpe data.frame
BedpeInteractionsTrack-class BedpeInteractionsTrack: paired-end interactions from a bedpe data.frame
checkReferenceCompatibility Check reference compatibility between track data and genome specification
CramTrack Alignment tracks: in-memory reads, a bam url or a cram url
CramTrack-class Alignment tracks: in-memory reads, a bam url or a cram url
DataFrameAnnotationTrack Annotation tracks: bed-like features from a data.frame, GRanges or UCSCData
DataFrameAnnotationTrack-class Annotation tracks: bed-like features from a data.frame, GRanges or UCSCData
DataFrameQuantitativeTrack Quantitative tracks: scored intervals from a data.frame, GRanges or UCSCData
DataFrameQuantitativeTrack-class Quantitative tracks: scored intervals from a data.frame, GRanges or UCSCData
display display the already constructed and configured track
display-method display the already constructed and configured track
GenomicAlignmentTrack Alignment tracks: in-memory reads, a bam url or a cram url
GenomicAlignmentTrack-class Alignment tracks: in-memory reads, a bam url or a cram url
getGenomicRegion focus igv on a region
getGenomicRegion-method 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
GFF3Track GFF3Track: gene models from a GFF3 data.frame or url
GFF3Track-class GFF3Track: gene models from a GFF3 data.frame or url
GRangesAnnotationTrack Annotation tracks: bed-like features from a data.frame, GRanges or UCSCData
GRangesAnnotationTrack-class Annotation tracks: bed-like features from a data.frame, GRanges or UCSCData
GRangesQuantitativeTrack Quantitative tracks: scored intervals from a data.frame, GRanges or UCSCData
GRangesQuantitativeTrack-class Quantitative tracks: scored intervals from a data.frame, GRanges or UCSCData
GWASTrack Constructor for GWASTrack
GWASTrack-class Constructor for GWASTrack
igvAnnotationTrack Build an annotation track from whatever annotation object is at hand
igvAnnotationTrack-class Annotation tracks: bed-like features from a data.frame, GRanges or UCSCData
igvShiny Create an igvShiny instance
igvShinyOutput create the UI for the widget
loadBamTrackFromLocalData load GenomicAlignments data as an igv.js alignment track
loadBamTrackFromLocalFile Load a BAM Track from a Local File via HTTP Range Requests
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
loadCramTrackFromLocalFile 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
loadTrack Display a track object in an igvShiny widget
loadTrack-method Display a track object in an igvShiny widget
loadVcfTrack load a VCF (variant) track provided as a Bioconductor VariantAnnotation object
parseAndValidateGenomeSpec parseAndValidateGenomeSpec
QuantitativeTrack Quantitative tracks: scored intervals from a data.frame, GRanges or UCSCData
QuantitativeTrack-class Quantitative tracks: scored intervals from a data.frame, GRanges or UCSCData
RemoteAlignmentTrack Alignment tracks: in-memory reads, a bam url or a cram url
RemoteAlignmentTrack-class Alignment tracks: in-memory reads, a bam url or a cram url
removeTracksByName remove tracks from the browser
removeTracksByName-method remove tracks from the browser
removeUserAddedTracks remove only those tracks explicitly added by your app
renderIgvShiny draw the igv genome browser element
serveLocalFile Serve a local file via HTTP Range Requests from the Shiny session
show-method Print a summary of a track object
show-method Display a short summary of a GWASTrack object
showGenomicRegion focus igv on a region
showGenomicRegion-method focus igv on a region
Track Track: the base class of igvShiny's S4 tracks
Track-class Track: the base class of igvShiny's S4 tracks
trackInfo Basic facts about a track
trackInfo-method Basic facts about a track
trackSize Basic facts about a track
trackSize-method Basic facts about a track
UCSCBedAnnotationTrack Annotation tracks: bed-like features from a data.frame, GRanges or UCSCData
UCSCBedAnnotationTrack-class Annotation tracks: bed-like features from a data.frame, GRanges or UCSCData
UCSCBedGraphQuantitativeTrack Quantitative tracks: scored intervals from a data.frame, GRanges or UCSCData
UCSCBedGraphQuantitativeTrack-class Quantitative tracks: scored intervals from a data.frame, GRanges or UCSCData
VariantTrack VariantTrack: variants from a VariantAnnotation VCF object
VariantTrack-class VariantTrack: variants from a VariantAnnotation VCF object