R interface to genome annotation files and the UCSC genome browser


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Documentation for package ‘rtracklayer’ version 1.54.0

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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 Quickload Access
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