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

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

## Documentation for package ‘rtracklayer’ version 1.64.0

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

## Help Pages

A B C D E F G H 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
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"
BBFile | BigBed Import and Export
BBFile-class | BigBed Import and Export
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
BigBedFile | BigBed Import and Export
BigBedFile-class | BigBed Import and Export
BigBedSelection | Selection of ranges and columns
BigBedSelection-class | Selection of ranges and columns
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
BroadPeakFile | BEDFile objects
BroadPeakFile-class | BEDFile objects
browseGenome | Browse a genome
browseGenome-method | Browse a genome
browserSession | Get a genome browser session
BrowserSession-class | Class "BrowserSession"
browserSession-method | Get a genome browser session
browserSession-methods | Get a genome browser session
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:BBFile | BigBed Import and Export
class:BED15File | BEDFile objects
class:BEDFile | BEDFile objects
class:BEDGraphFile | BEDFile objects
class:BigBedFile | BigBed Import and Export
class:BigWigFile | BigWig Import and Export
class:BigWigFileList | BigWig Import and Export
class:BroadPeakFile | BEDFile objects
class:BWFile | BigWig Import and Export
class:Chain | Chain objects
class:ChainBlock | Chain objects
class:ChainFile | Chain 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:NarrowPeakFile | BEDFile objects
class:Quickload | Quickload Access
class:QuickloadGenome | Quickload Genome Access
class:TrackDb | Track Databases
class:TrackHub | TrackHub Access
class:TrackHubGenome | TrackHub Genome Access
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 | Selection of ranges and columns
coerce-method | Quickload Access
coerce-method | TrackHub Access
coerce-method | Class "UCSCData"
coerce-method | Class "BasicTrackLine"
coerce-method | Class "TrackLine"
coerce-method | Class "GraphTrackLine"
cpneTrack | CPNE1 SNP track

## -- D --

descriptionUrl-method | TrackHub Access
descriptionUrl<--method | TrackHub Access

## -- E --

email-method | TrackHub Access
email<--method | TrackHub Access
export-method | BEDFile objects
export-method | Export to BAM Files
export-method | BigBed Import and Export
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.2bit | 2bit Files
export.2bit-method | 2bit Files
export.bb | BigBed Import and Export
export.bb-method | BigBed Import and Export
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

## -- G --

genome-method | GFFFile objects
genome-method | Quickload Access
genome-method | Quickload Genome Access
genome-method | TrackHub Access
genome-method | TrackHub Genome Access
genome-method | UCSC Schema
genome-method | Querying UCSC Tables
genome-method | Class "BrowserSession"
genome-method | Class "UCSCSession"
genome<--method | Querying UCSC Tables
genome<--method | Class "BrowserSession"
genome<--method | Class "UCSCSession"
genomeBrowsers | Get available genome browsers
genomeField-method | TrackHub Access
genomeField<--method | TrackHub Access
genomeFile-method | TrackHub Access
genomeFile<--method | TrackHub Access
genomeInfo-method | TrackHub Access
genomeInfo<--method | TrackHub Access
GenomicData | Data on a Genome
GenomicSelection | Genomic data selection
getSeq-method | 2bit Files
getTable | Querying UCSC Tables
getTable-method | Querying UCSC Tables
getTable-method | Class "UCSCSession"
getTracks-method | TrackHub Genome Access
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

## -- H --

hub-method | TrackHub Access
hub<--method | TrackHub Access
hubUrl | Querying UCSC Tables
hubUrl-method | Querying UCSC Tables
hubUrl<--method | Querying UCSC Tables

## -- I --

import-method | BEDFile objects
import-method | Export to BAM Files
import-method | BigBed Import and Export
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.2bit | 2bit Files
import.2bit-method | 2bit Files
import.bb | BigBed Import and Export
import.bb-method | BigBed Import and Export
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.BroadPeak | BEDFile objects
import.BroadPeak-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.NarrowPeak | BEDFile objects
import.NarrowPeak-method | BEDFile 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"
IntegerRangesList-methods | Ranges on a Genome

## -- L --

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

## -- M --

mcols-method | Quickload Genome Access

## -- N --

names-method | Quickload Genome Access
names-method | TrackHub Genome Access
names-method | Querying UCSC Tables
names-method | Class "BrowserSession"
names<--method | Querying UCSC Tables
NarrowPeakFile | BEDFile objects
NarrowPeakFile-class | BEDFile objects
nrow-method | UCSC Schema

## -- O --

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

## -- P --

path-method | BigWig Import and Export

## -- 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
readGFF | Reads a file in GFF format
referenceSequence | Quickload Genome Access
referenceSequence-method | Quickload Genome Access
referenceSequence-method | TrackHub Genome Access
referenceSequence<- | Quickload Genome Access
referenceSequence<--method | Quickload Genome Access
referenceSequence<--method | TrackHub Genome Access
releaseDate-method | Quickload Genome Access
reversed | Chain objects
reversed-method | Chain objects

## -- S --

score-method | Chain objects
score-method | Data on a Genome
seqinfo-method | BigBed Import and Export
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
shortLabel-method | TrackHub Access
shortLabel<--method | TrackHub Access
show-method | Quickload Access
show-method | Quickload Genome Access
show-method | TrackHub Access
show-method | TrackHub Genome Access
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 | TrackHub 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 | TrackHub Genome Access
track<--method | Laying tracks
track<--method | Class "UCSCSession"
track<--methods | Laying tracks
TrackDb-class | Track Databases
trackField-method | TrackHub Genome Access
trackField<--method | TrackHub Genome Access
TrackHub | TrackHub Access
trackhub | TrackHub Genome Access
TrackHub-class | TrackHub Access
TrackHubGenome | TrackHub Genome Access
TrackHubGenome-class | TrackHub Genome Access
TrackLine-class | Class "TrackLine"
trackNames | Accessing track names
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
ucscTables | 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 | TrackHub Access
uri-method | Quickload Genome Access
uri-method | TrackHub Genome Access

## -- V --

viewURL | Class "UCSCView"
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
writeTrackHub | TrackHub Access
writeTrackHub-method | TrackHub Genome Access

## -- misc --

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