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