# R interface to genome annotation files and the UCSC genome browser

## Documentation for package ‘rtracklayer’ version 1.38.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

A B C E F G I L M N O P Q R S T U V W misc

## -- A --

activeView | Accessing the active view
activeView-method | Accessing the active view
activeView-methods | Accessing the active view
activeView<- | Accessing the active view
activeView<--methods | Accessing the active view
as.character-method | RTLFile objects
asBED | Coerce to BED structure
asBED-method | Coerce to BED structure
asGFF | Coerce to GFF structure
asGFF-method | Coerce to GFF structure

## -- B --

BasicTrackLine-class | Class "BasicTrackLine"
BED15File | BEDFile objects
BED15File-class | BEDFile objects
Bed15TrackLine-class | Class "Bed15TrackLine"
BEDFile | BEDFile objects
BEDFile-class | BEDFile objects
BEDGraphFile | BEDFile objects
BEDGraphFile-class | BEDFile objects
BEDPEFile | BEDFile objects
BEDPEFile-class | BEDFile objects
BigWigFile | BigWig Import and Export
BigWigFile-class | BigWig Import and Export
BigWigFileList | BigWig Import and Export
BigWigFileList-class | BigWig Import and Export
BigWigSelection | Selection of ranges and columns
BigWigSelection-class | Selection of ranges and columns
blocks | Get blocks/exons
blocks-method | Get blocks/exons
blocks-methods | Get blocks/exons
browseGenome | Browse a genome
browseGenome-method | Browse a genome
browserSession | Get a genome browser session
BrowserSession-class | Class "BrowserSession"
browserSession-method | Querying UCSC Tables
browserSession-method | Get a genome browser session
browserSession-methods | Get a genome browser session
browserSession<- | Querying UCSC Tables
browserSession<--method | Querying UCSC Tables
browserView | Getting browser views
BrowserView-class | Class "BrowserView"
browserView-method | Getting browser views
browserView-methods | Getting browser views
BrowserViewList | Lists of BrowserView
BrowserViewList-class | Lists of BrowserView
browserViews | Getting the browser views
browserViews-method | Getting the browser views
browserViews-methods | Getting the browser views
BWFile | BigWig Import and Export
BWFile-class | BigWig Import and Export

## -- C --

Chain-class | Chain objects
ChainBlock-class | Chain objects
ChainFile | Chain objects
ChainFile-class | Chain objects
chrom | Data on a Genome
chrom-method | Data on a Genome
chrom-method | Ranges on a Genome
chrom<- | Data on a Genome
chrom<--method | Data on a Genome
chrom<--method | Ranges on a Genome
class:2BitFile | 2bit Files
class:BED15File | BEDFile objects
class:BEDFile | BEDFile objects
class:BEDGraphFile | BEDFile objects
class:BigWigFile | BigWig Import and Export
class:BigWigFileList | BigWig Import and Export
class:BWFile | BigWig Import and Export
class:Chain | Chain objects
class:ChainBlock | Chain objects
class:ChainFile | Chain objects
class:CompressedFile | RTLFile objects
class:FastaFile | FastaFile objects
class:GFF1File | GFFFile objects
class:GFF2File | GFFFile objects
class:GFF3File | GFFFile objects
class:GFFFile | GFFFile objects
class:GTFFile | GFFFile objects
class:GVFFile | GFFFile objects
class:Quickload | Quickload Access
class:QuickloadGenome | Quickload Genome Access
class:RTLFile | RTLFile objects
class:TrackDb | Track Databases
class:TwoBitFile | 2bit Files
class:UCSCFile | UCSCFile objects
class:WIGFile | WIG Import and Export
cleanupBigWigCache | BigWig Import and Export
coerce-method | Class "Bed15TrackLine"
coerce-method | Selection of ranges and columns
coerce-method | Quickload Access
coerce-method | Class "UCSCData"
coerce-method | Class "BasicTrackLine"
coerce-method | Class "TrackLine"
coerce-method | Class "GraphTrackLine"
CompressedFile-class | RTLFile objects
cpneTrack | CPNE1 SNP track

## -- E --

export | Import and export
export-method | BEDFile objects
export-method | Export to BAM Files
export-method | BigWig Import and Export
export-method | FastaFile objects
export-method | GFFFile objects
export-method | TabixFile Import/Export
export-method | 2bit Files
export-method | UCSCFile objects
export-method | WIG Import and Export
export-method | Import and export
export.2bit | 2bit Files
export.2bit-method | 2bit Files
export.bed | BEDFile objects
export.bed-method | BEDFile objects
export.bed-method | Class "UCSCData"
export.bed15 | BEDFile objects
export.bed15-method | BEDFile objects
export.bed15-method | Class "UCSCData"
export.bedGraph | BEDFile objects
export.bedGraph-method | BEDFile objects
export.bw | BigWig Import and Export
export.bw-method | BigWig Import and Export
export.gff | GFFFile objects
export.gff-method | GFFFile objects
export.gff-method | Class "UCSCData"
export.gff1 | GFFFile objects
export.gff1-method | GFFFile objects
export.gff2 | GFFFile objects
export.gff2-method | GFFFile objects
export.gff3 | GFFFile objects
export.gff3-method | GFFFile objects
export.ucsc | UCSCFile objects
export.ucsc-method | Class "UCSCData"
export.ucsc-method | UCSCFile objects
export.wig | WIG Import and Export
export.wig-method | WIG Import and Export
exportToTabix | TabixFile Import/Export
exportToTabix-method | TabixFile Import/Export

## -- F --

FastaFile | FastaFile objects
FastaFile-class | FastaFile objects
FileForFormat | RTLFile objects
formatDescription | UCSC Schema
formatDescription-method | UCSC Schema

## -- G --

genome-method | GFFFile objects
genome-method | Quickload Access
genome-method | Quickload Genome Access
genome-method | UCSC Schema
genome-method | Class "BrowserSession"
genome-method | Class "UCSCSession"
genome<--method | Class "BrowserSession"
genome<--method | Class "UCSCSession"
genomeBrowsers | Get available genome browsers
GenomicData | Data on a Genome
GenomicRanges_OR_GenomicRangesList-class | Browse a genome
GenomicSelection | Genomic data selection
getSeq-method | 2bit Files
getTable | Querying UCSC Tables
getTable-method | Querying UCSC Tables
getTable-method | Class "UCSCSession"
GFF1File | GFFFile objects
GFF1File-class | GFFFile objects
GFF2File | GFFFile objects
GFF2File-class | GFFFile objects
GFF3File | GFFFile objects
GFF3File-class | GFFFile objects
GFFcolnames | Reads a file in GFF format
GFFFile | GFFFile objects
GFFFile-class | GFFFile objects
GRangesForBSGenome | GRanges for a Genome
GRangesForUCSCGenome | GRanges for a Genome
GraphTrackLine-class | Class "GraphTrackLine"
GTFFile | GFFFile objects
GTFFile-class | GFFFile objects
GVFFile | GFFFile objects
GVFFile-class | GFFFile objects

## -- I --

import | Import and export
import-method | BEDFile objects
import-method | Export to BAM Files
import-method | BigWig Import and Export
import-method | Chain objects
import-method | FastaFile objects
import-method | GFFFile objects
import-method | TabixFile Import/Export
import-method | 2bit Files
import-method | UCSCFile objects
import-method | WIG Import and Export
import-method | Import and export
import.2bit | 2bit Files
import.2bit-method | 2bit Files
import.bed | BEDFile objects
import.bed-method | BEDFile objects
import.bed15 | BEDFile objects
import.bed15-method | BEDFile objects
import.bedGraph | BEDFile objects
import.bedGraph-method | BEDFile objects
import.bw | BigWig Import and Export
import.bw-method | BigWig Import and Export
import.chain | Chain objects
import.chain-method | Chain objects
import.gff | GFFFile objects
import.gff-method | GFFFile objects
import.gff1 | GFFFile objects
import.gff1-method | GFFFile objects
import.gff2 | GFFFile objects
import.gff2-method | GFFFile objects
import.gff3 | GFFFile objects
import.gff3-method | GFFFile objects
import.ucsc | UCSCFile objects
import.ucsc-method | UCSCFile objects
import.wig | WIG Import and Export
import.wig-method | WIG Import and Export
initialize-method | Class "UCSCData"
initialize-method | Class "UCSCSession"

## -- L --

length-method | Quickload Access
length-method | Quickload Genome Access
liftOver | Lift intervals between genome builds
liftOver-method | Lift intervals between genome builds

## -- M --

mcols-method | Quickload Genome Access

## -- N --

names-method | Quickload Genome Access
names-method | Querying UCSC Tables
names-method | Class "BrowserSession"
names<--method | Querying UCSC Tables
nrow-method | UCSC Schema

## -- O --

offset-method | Chain objects
organism-method | Quickload Genome Access

## -- P --

path | RTLFile objects
path-method | BigWig Import and Export
path-method | RTLFile objects

## -- Q --

Quickload | Quickload Access
quickload | Quickload Genome Access
Quickload-class | Quickload Access
QuickloadGenome | Quickload Genome Access
QuickloadGenome-class | Quickload Genome Access

## -- R --

range-method | Querying UCSC Tables
range-method | Class "BrowserSession"
range-method | Class "UCSCSession"
range-method | Class "UCSCView"
range<- | Class "UCSCSession"
range<--method | Querying UCSC Tables
range<--method | Class "UCSCSession"
range<--method | Class "UCSCView"
ranges-method | Chain objects
RangesList-methods | Ranges on a Genome
readGFF | Reads a file in GFF format
referenceSequence | Quickload Genome Access
referenceSequence-method | Quickload Genome Access
referenceSequence<- | Quickload Genome Access
referenceSequence<--method | Quickload Genome Access
releaseDate-method | Quickload Genome Access
resource | RTLFile objects
reversed | Chain objects
reversed-method | Chain objects
RTLFile-class | RTLFile objects
RTLFileList-class | RTLFile objects

## -- S --

score-method | Chain objects
score-method | Data on a Genome
seqinfo-method | BigWig Import and Export
seqinfo-method | Quickload Genome Access
seqinfo-method | 2bit Files
seqinfo-method | Class "UCSCSession"
seqinfo<--method | Quickload Genome Access
SeqinfoForBSGenome | GRanges for a Genome
SeqinfoForUCSCGenome | GRanges for a Genome
sequence<- | Load a sequence
sequence<--methods | Load a sequence
show-method | Quickload Access
show-method | Quickload Genome Access
show-method | RTLFile objects
show-method | Class "UCSCData"
show-method | Querying UCSC Tables
show-method | Class "BrowserSession"
show-method | Class "BrowserView"
show-method | Class "TrackLine"
space-method | Chain objects
split-method | Class "UCSCData"
summary-method | BigWig Import and Export

## -- T --

tableName | Querying UCSC Tables
tableName-method | UCSC Schema
tableName-method | Querying UCSC Tables
tableName<- | Querying UCSC Tables
tableName<--method | Querying UCSC Tables
tableNames | Querying UCSC Tables
tableNames-method | Querying UCSC Tables
targets | microRNA target sites
track | Querying UCSC Tables
track-method | Quickload Genome Access
track-method | Querying UCSC Tables
track-method | Class "UCSCSession"
track<- | Laying tracks
track<--method | Quickload Genome Access
track<--method | Track Databases
track<--method | Laying tracks
track<--method | Class "UCSCSession"
track<--methods | Laying tracks
TrackDb-class | Track Databases
TrackLine-class | Class "TrackLine"
trackName | Querying UCSC Tables
trackName-method | Querying UCSC Tables
trackName<- | Querying UCSC Tables
trackName<--method | Querying UCSC Tables
trackNames | Accessing track names
trackNames-method | Querying UCSC Tables
trackNames-method | Class "BrowserSession"
trackNames-method | Accessing track names
trackNames-methods | Accessing track names
trackNames<- | Accessing track names
trackNames<--method | Accessing track names
trackNames<--methods | Accessing track names
TwoBitFile | 2bit Files
TwoBitFile-class | 2bit Files

## -- U --

UCSCData-class | Class "UCSCData"
UCSCFile | UCSCFile objects
UCSCFile-class | UCSCFile objects
ucscGenomes | Get available genomes on UCSC
ucscSchema | Querying UCSC Tables
UCSCSchema-class | UCSC Schema
ucscSchema-method | UCSC Schema
ucscSchema-method | Querying UCSC Tables
UCSCSession-class | Class "UCSCSession"
ucscTableQuery | Querying UCSC Tables
UCSCTableQuery-class | Querying UCSC Tables
ucscTableQuery-method | Querying UCSC Tables
ucscTrackModes | Accessing UCSC track modes
UCSCTrackModes-class | Class "UCSCTrackModes"
ucscTrackModes-method | Accessing UCSC track modes
ucscTrackModes-methods | Accessing UCSC track modes
ucscTrackModes<- | Accessing UCSC track modes
ucscTrackModes<--method | Accessing UCSC track modes
ucscTrackModes<--methods | Accessing UCSC track modes
UCSCView-class | Class "UCSCView"
uri | Quickload Access
uri-method | Quickload Genome Access

## -- V --

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

## -- W --

WIGFile | WIG Import and Export
WIGFile-class | WIG Import and Export
wigToBigWig | Convert WIG to BigWig

## -- misc --

$-method | Quickload Access
$-method | Track Databases
$<--method | Track Databases
2BitFile | 2bit Files
2BitFile-class | 2bit Files
[-method | Class "UCSCTrackModes"
[<--method | Class "UCSCTrackModes"
[[-method | Quickload Access
[[-method | Track Databases
[[<--method | Track Databases