R interface to genome browsers and their annotation tracks


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Documentation for package ‘rtracklayer’ version 1.2.2

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A B C D E G I L M S T U W misc

*,genomeSegment,ANY-method Class "genomeSegment"
/,genomeSegment,ANY-method Class "genomeSegment"

-- A --

activeView Accessing the active view
activeView,argoSession-method Accessing the active view
activeView,argoView-method Accessing the active view
activeView,browserSession-method Accessing the active view
activeView,ucscView-method Accessing the active view
activeView-methods Accessing the active view
activeView<-,argoSession-method Accessing the active view
activeView<--methods Accessing the active view
argoSession-class Class "argoSession"
argoView-class Class "argoView"

-- B --

basicTrackLine-class Class "basicTrackLine"
browseGenome Browse a genome
browseGenome,ANY-method Browse a genome
browserSession Get a genome browser session
browserSession,browserView-method Get a genome browser session
browserSession,character-method Get a genome browser session
browserSession,missing-method Get a genome browser session
browserSession-class Class "browserSession"
browserSession-methods Get a genome browser session
browserView Getting browser views
browserView,argoSession-method Getting browser views
browserView,ucscSession-method Getting browser views
browserView-class Class "browserView"
browserView-methods Getting browser views
browserViews Getting the browser views
browserViews,argoSession-method Getting the browser views
browserViews,ucscSession-method Getting the browser views
browserViews-methods Getting the browser views

-- C --

chrid Getting chromosome ids
chrid,ANY-method Getting chromosome ids
chrid,character-method Getting chromosome ids
chrid,trackSet-method Getting chromosome ids
chrid-class Class "chrid"
chrid-methods Getting chromosome ids
chrom,genomeSegment-method Class "genomeSegment"
chrom,trackSet-method Class "trackSet"
chrom<-,genomeSegment-method Class "genomeSegment"
close,argoSession-method Class "argoSession"
close,argoView-method Class "argoView"
coerce,basicTrackLine,character-method Class "basicTrackLine"
coerce,basicTrackLine,wigTrackLine-method Class "wigTrackLine"
coerce,character,basicTrackLine-method Class "basicTrackLine"
coerce,character,ucscTrackLine-method Class "ucscTrackLine"
coerce,character,wigTrackLine-method Class "wigTrackLine"
coerce,trackSet,data.frame-method Class "trackSet"
coerce,ucscTrackLine,character-method Class "ucscTrackLine"
coerce,wigTrackLine,basicTrackLine-method Class "wigTrackLine"
coerce,wigTrackLine,character-method Class "wigTrackLine"
cpneTrack CPNE1 SNP track

-- D --

dataVals Get data values
dataVals,trackSet-method Get data values
dataVals-methods Get data values

-- E --

end,genomeSegment-method Class "genomeSegment"
end,trackSet-method Class "trackSet"
end<-,genomeSegment-method Class "genomeSegment"
export Export objects to connections
export,ANY,ANY,character-method Export objects to connections
export,ANY,character,character-method Export objects to connections
export,ANY,character,missing-method Export objects to connections
export,ANY,missing,character-method Export objects to connections
export.bed Export tracks
export.bed,trackSet-method Export tracks
export.bed,ucscTrackSet-method Class "ucscTrackSet"
export.gff Export tracks
export.gff,trackSet-method Export tracks
export.gff,ucscTrackSet-method Class "ucscTrackSet"
export.gff1 Export tracks
export.gff1,ANY-method Export tracks
export.gff2 Export tracks
export.gff2,ANY-method Export tracks
export.gff3 Export tracks
export.gff3,ANY-method Export tracks
export.ucsc Export tracks
export.ucsc,trackSet-method Export tracks
export.ucsc,trackSets-method Export tracks
export.ucsc,ucscTrackSet-method Class "ucscTrackSet"
export.wig Export tracks
export.wig,trackSet-method Export tracks

-- G --

genome,genomeSegment-method Class "genomeSegment"
genome,trackSet-method Class "trackSet"
genome<-,genomeSegment-method Class "genomeSegment"
genomeBrowsers Get available genome browsers
genomeSegment Accessing a segment of a genome
genomeSegment,argoView-method Accessing a segment of a genome
genomeSegment,browserSession-method Accessing a segment of a genome
genomeSegment,character-method Accessing a segment of a genome
genomeSegment,IRanges-method Accessing a segment of a genome
genomeSegment,missing-method Accessing a segment of a genome
genomeSegment,trackSet-method Accessing a segment of a genome
genomeSegment,trackSets-method Accessing a segment of a genome
genomeSegment,ucscCart-method Accessing a segment of a genome
genomeSegment,ucscSession-method Accessing a segment of a genome
genomeSegment,ucscView-method Accessing a segment of a genome
genomeSegment-class Class "genomeSegment"
genomeSegment-methods Accessing a segment of a genome
genomeSegment<-,argoView-method Accessing a segment of a genome
genomeSegment<-,ucscView-method Accessing a segment of a genome
genomeSequence Retrieving a genome sequence
genomeSequence,argoSession-method Retrieving a genome sequence
genomeSequence,ucscSession-method Retrieving a genome sequence
genomeSequence-methods Retrieving a genome sequence

-- I --

import Importing objects
import,ANY,character,ANY-method Importing objects
import,character,character,ANY-method Importing objects
import,character,missing,ANY-method Importing objects
import,missing,ANY,character-method Importing objects
import.bed Importing tracks
import.bed,ANY-method Importing tracks
import.gff Importing tracks
import.gff,ANY-method Importing tracks
import.gff1 Importing tracks
import.gff1,ANY-method Importing tracks
import.gff2 Importing tracks
import.gff2,ANY-method Importing tracks
import.gff3 Importing tracks
import.gff3,ANY-method Importing tracks
import.ucsc Importing tracks
import.ucsc,ANY-method Importing tracks
import.wig Importing tracks
import.wig,ANY-method Importing tracks
initialize,argoSession-method Class "argoSession"
initialize,trackSet-method Class "trackSet"
initialize,ucscSession-method Class "ucscSession"
initialize,ucscTrackSet-method Class "ucscTrackSet"

-- L --

laySequence Load a sequence
laySequence,argoSession,character-method Load a sequence
laySequence-methods Load a sequence
layTrack Laying tracks
layTrack,argoSession,trackSet-method Laying tracks
layTrack,browserSession,trackSet-method Laying tracks
layTrack,browserSession,trackSets-method Laying tracks
layTrack,ucscSession,trackSets-method Laying tracks
layTrack-methods Laying tracks

-- M --

merge,genomeSegment,genomeSegment-method Class "genomeSegment"

-- S --

show,browserSession-method Class "browserSession"
show,browserView-method Class "browserView"
show,trackSet-method Class "trackSet"
show,ucscTrackLine-method Class "ucscTrackLine"
show,ucscTrackSet-method Class "ucscTrackSet"
start,genomeSegment-method Class "genomeSegment"
start,trackSet-method Class "trackSet"
start<-,genomeSegment-method Class "genomeSegment"
strand,trackSet-method Class "trackSet"

-- T --

trackData Get track data
trackData,trackSet-method Get track data
tracks Accessing track names
tracks,argoSession-method Accessing track names
tracks,argoView-method Accessing track names
tracks,ucscSession-method Accessing track names
tracks,ucscTrackModes-method Accessing track names
tracks,ucscView-method Accessing track names
tracks-methods Accessing track names
tracks<-,argoView-method Accessing track names
tracks<-,ucscTrackModes-method Accessing track names
tracks<-,ucscView-method Accessing track names
tracks<--methods Accessing track names
trackSet Get a trackSet
trackSet,AnnotatedDataFrame-method Get a trackSet
trackSet,argoSession-method Get a trackSet
trackSet,character-method Get a trackSet
trackSet,data.frame-method Get a trackSet
trackSet,IRanges-method Get a trackSet
trackSet,ucscSession-method Get a trackSet
trackSet-class Class "trackSet"
trackSet-methods Get a trackSet
trackSets Getting a list of trackSets
trackSets,list-method Getting a list of trackSets
trackSets,missing-method Getting a list of trackSets
trackSets,trackSet-method Getting a list of trackSets
trackSets-class Class "trackSets"
trackSets-methods Getting a list of trackSets

-- U --

ucscSession-class Class "ucscSession"
ucscTable Get a database table from UCSC
ucscTable,ucscSession-method Get a database table from UCSC
ucscTrackLine-class Class "ucscTrackLine"
ucscTrackModes Accessing UCSC track modes
ucscTrackModes,character-method Accessing UCSC track modes
ucscTrackModes,missing-method Accessing UCSC track modes
ucscTrackModes,ucscSession-method Accessing UCSC track modes
ucscTrackModes,ucscTracks-method Accessing UCSC track modes
ucscTrackModes,ucscView-method Accessing UCSC track modes
ucscTrackModes-class Class "ucscTrackModes"
ucscTrackModes-methods Accessing UCSC track modes
ucscTrackModes<-,ucscView,character-method Accessing UCSC track modes
ucscTrackModes<-,ucscView,ucscTrackModes-method Accessing UCSC track modes
ucscTrackModes<--methods Accessing UCSC track modes
ucscTrackSet-class Class "ucscTrackSet"
ucscView-class Class "ucscView"

-- W --

wigTrackLine-class Class "wigTrackLine"

-- misc --

[,trackSet,ANY,ANY,ANY-method Class "trackSet"
[,ucscTrackModes,ANY,ANY,ANY-method Class "ucscTrackModes"
[.trackSet Class "trackSet"
[<-,ucscTrackModes,ANY,ANY,ANY-method Class "ucscTrackModes"