# R interface to genome browsers and their annotation tracks

## Documentation for package ‘rtracklayer’ version 1.6.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A B C E G I N R S T U V misc

## -- --

$,BrowserSession-method | Class "BrowserSession"
$<-,BrowserSession,ANY,RangedDataORRangedDataList-method | Class "BrowserSession"

## -- A --

activeView | 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<- | Accessing the active view
activeView<--methods | Accessing the active view

## -- B --

BasicTrackLine-class | Class "BasicTrackLine"
Bed15TrackLine-class | Class "Bed15TrackLine"
blocks | Get blocks/exons
blocks,RangedData-method | Get blocks/exons
blocks-methods | Get blocks/exons
browseGenome | Browse a genome
browseGenome,missing-method | Browse a genome
browseGenome,RangedDataORRangedDataList-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,UCSCTableQuery-method | Querying UCSC Tables
BrowserSession-class | Class "BrowserSession"
browserSession-methods | Get a genome browser session
browserSession<- | Querying UCSC Tables
browserSession<-,UCSCTableQuery,UCSCSession-method | Querying UCSC Tables
browserView | Getting browser views
browserView,UCSCSession-method | Getting browser views
BrowserView-class | Class "BrowserView"
browserView-methods | Getting browser views
browserViews | Getting the browser views
browserViews,UCSCSession-method | Getting the browser views
browserViews-methods | Getting the browser views

## -- C --

chrom | Data on a Genome
chrom,RangedData-method | Data on a Genome
chrom,RangesList-method | Ranges on a Genome
chrom<- | Data on a Genome
chrom<-,RangedData-method | Data on a Genome
chrom<-,RangesList-method | Ranges on a Genome
coerce,BasicTrackLine,character-method | Class "BasicTrackLine"
coerce,BasicTrackLine,GraphTrackLine-method | Class "GraphTrackLine"
coerce,Bed15TrackLine,character-method | Class "Bed15TrackLine"
coerce,character,BasicTrackLine-method | Class "BasicTrackLine"
coerce,character,Bed15TrackLine-method | Class "Bed15TrackLine"
coerce,character,GraphTrackLine-method | Class "GraphTrackLine"
coerce,character,TrackLine-method | Class "TrackLine"
coerce,GraphTrackLine,BasicTrackLine-method | Class "GraphTrackLine"
coerce,GraphTrackLine,character-method | Class "GraphTrackLine"
coerce,RangedData,UCSCData-method | Class "UCSCData"
coerce,TrackLine,character-method | Class "TrackLine"
cpneTrack | CPNE1 SNP track

## -- E --

export | Export objects to connections
export,ANY,character,character-method | Export objects to connections
export,ANY,character,missing-method | Export objects to connections
export,ANY,connection,character-method | Export objects to connections
export,ANY,missing,character-method | Export objects to connections
export.bed | Export tracks
export.bed,ANY,ANY-method | Export tracks
export.bed,RangedData,characterORconnection-method | Export tracks
export.bed,RangedDataList,ANY-method | Export tracks
export.bed,UCSCData,ANY-method | Class "UCSCData"
export.bed15 | Export tracks
export.bed15,ANY-method | Export tracks
export.bed15,UCSCData-method | Class "UCSCData"
export.bedGraph | Export tracks
export.bedGraph,ANY-method | Export tracks
export.gff | Export tracks
export.gff,ANY,ANY-method | Export tracks
export.gff,RangedData,characterORconnection-method | Export tracks
export.gff,UCSCData,characterORconnection-method | Class "UCSCData"
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,ANY,ANY-method | Export tracks
export.ucsc,RangedData,ANY-method | Export tracks
export.ucsc,RangedDataList,ANY-method | Export tracks
export.ucsc,UCSCData,characterORconnection-method | Class "UCSCData"
export.wig | Export tracks
export.wig,ANY-method | Export tracks

## -- G --

genome | Data on a Genome
genome,BrowserSession-method | Class "BrowserSession"
genome,RangedData-method | Data on a Genome
genome,RangesList-method | Ranges on a Genome
genome,UCSCSession-method | Class "UCSCSession"
genome<- | Data on a Genome
genome<-,BrowserSession-method | Class "BrowserSession"
genome<-,RangedData-method | Data on a Genome
genome<-,RangesList-method | Ranges on a Genome
genome<-,UCSCSession-method | Class "UCSCSession"
genomeBrowsers | Get available genome browsers
GenomicData | Data on a Genome
GenomicRanges | Ranges on a Genome
getSeq,UCSCSession-method | Retrieving a genome sequence
getTable | Querying UCSC Tables
getTable,UCSCTableQuery-method | Querying UCSC Tables
GraphTrackLine-class | Class "GraphTrackLine"

## -- I --

import | Importing objects
import,character,character,ANY-method | Importing objects
import,character,missing,ANY-method | Importing objects
import,connection,character,ANY-method | Importing objects
import,missing,ANY,character-method | Importing objects
import.bed | Importing tracks
import.bed,connection-method | Importing tracks
import.bed15 | Importing tracks
import.bed15,ANY-method | Importing tracks
import.bedGraph | Importing tracks
import.bedGraph,ANY-method | Importing tracks
import.gff | Importing tracks
import.gff,characterORconnection-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,characterORconnection-method | Importing tracks
import.wig | Importing tracks
import.wig,ANY-method | Importing tracks
initialize,UCSCData-method | Class "UCSCData"
initialize,UCSCSession-method | Class "UCSCSession"

## -- N --

names,UCSCTableQuery-method | Querying UCSC Tables
names<-,UCSCTableQuery-method | Querying UCSC Tables

## -- R --

range,BrowserSession-method | Class "BrowserSession"
range,ucscCart-method | Class "UCSCSession"
range,UCSCSession-method | Class "UCSCSession"
range,UCSCTableQuery-method | Querying UCSC Tables
range,UCSCView-method | Class "UCSCView"
range<- | Class "UCSCSession"
range<-,UCSCSession,RangesList-method | Class "UCSCSession"
range<-,UCSCTableQuery,RangesList-method | Querying UCSC Tables
range<-,UCSCView,RangesList-method | Class "UCSCView"
RangedData-methods | Data on a Genome
RangesList-methods | Ranges on a Genome

## -- S --

sequence<- | Load a sequence
sequence<--methods | Load a sequence
show,BrowserSession-method | Class "BrowserSession"
show,BrowserView-method | Class "BrowserView"
show,TrackLine-method | Class "TrackLine"
show,UCSCData-method | Class "UCSCData"
show,UCSCTableQuery-method | Querying UCSC Tables

## -- T --

tableName | Querying UCSC Tables
tableName,UCSCTableQuery-method | Querying UCSC Tables
tableName<- | Querying UCSC Tables
tableName<-,UCSCTableQuery-method | Querying UCSC Tables
tableNames | Querying UCSC Tables
tableNames,UCSCTableQuery-method | Querying UCSC Tables
targets | microRNA target sites
track | Querying UCSC Tables
track,UCSCSession-method | Class "UCSCSession"
track,UCSCTableQuery-method | Querying UCSC Tables
track<- | Laying tracks
track<-,BrowserSession,RangedData-method | Laying tracks
track<-,BrowserSession,RangedDataList-method | Laying tracks
track<-,UCSCSession,RangedDataList-method | Laying tracks
track<--methods | Laying tracks
TrackLine-class | Class "TrackLine"
trackName | Querying UCSC Tables
trackName,UCSCTableQuery-method | Querying UCSC Tables
trackName<- | Querying UCSC Tables
trackName<-,UCSCTableQuery-method | Querying UCSC Tables
trackNames | Accessing track names
trackNames,UCSCSession-method | Accessing track names
trackNames,UCSCTableQuery-method | Querying UCSC Tables
trackNames,UCSCTrackModes-method | Accessing track names
trackNames,UCSCView-method | Accessing track names
trackNames-methods | Accessing track names
trackNames<- | Accessing track names
trackNames<-,UCSCTrackModes-method | Accessing track names
trackNames<-,UCSCView-method | Accessing track names
trackNames<--methods | Accessing track names

## -- U --

UCSCData-class | Class "UCSCData"
ucscGenomes | Get available genomes on UCSC
UCSCSession-class | Class "UCSCSession"
ucscTableQuery | Querying UCSC Tables
ucscTableQuery,UCSCSession-method | Querying UCSC Tables
UCSCTableQuery-class | Querying UCSC Tables
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<- | 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
UCSCView-class | Class "UCSCView"

## -- V --

visible | Class "BrowserView"
visible,BrowserView-method | Class "BrowserView"
visible,UCSCView-method | Class "UCSCView"
visible<- | Class "BrowserView"
visible<-,BrowserView-method | Class "BrowserView"
visible<-,UCSCView-method | Class "UCSCView"

## -- misc --

[,UCSCTrackModes-method | Class "UCSCTrackModes"
[<-,UCSCTrackModes-method | Class "UCSCTrackModes"
[[,BrowserSession-method | Class "BrowserSession"
[[<-,BrowserSession,ANY,ANY,RangedDataORRangedDataList-method | Class "BrowserSession"