R interface to genome browsers and their annotation tracks

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Documentation for package ‘rtracklayer’ version 1.12.5

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A B C E F G I L N O R S T U V 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

-- B --

BasicTrackLine-class Class "BasicTrackLine"
Bed15TrackLine-class Class "Bed15TrackLine"
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

-- C --

Chain-class Chain objects
ChainBlock-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:Chain Chain objects
class:ChainBlock Chain objects
coerce-method Class "Bed15TrackLine"
coerce-method Selection of ranges and columns
coerce-method Class "UCSCData"
coerce-method Class "BasicTrackLine"
coerce-method Class "TrackLine"
coerce-method Class "GraphTrackLine"
cpneTrack CPNE1 SNP track

-- E --

export Export objects to connections
export-method Export objects to connections
export.bed Export tracks
export.bed-method Class "UCSCData"
export.bed-method Export tracks
export.bed15 Export tracks
export.bed15-method Class "UCSCData"
export.bed15-method Export tracks
export.bedGraph Export tracks
export.bedGraph-method Export tracks
export.bw Export tracks
export.bw-method Export tracks
export.gff Export tracks
export.gff-method Class "UCSCData"
export.gff-method Export tracks
export.gff1 Export tracks
export.gff1-method Export tracks
export.gff2 Export tracks
export.gff2-method Export tracks
export.gff3 Export tracks
export.gff3-method Export tracks
export.ucsc Export tracks
export.ucsc-method Class "UCSCData"
export.ucsc-method Export tracks
export.wig Export tracks
export.wig-method Export tracks

-- F --

formatDescription UCSC Schema
formatDescription-method UCSC Schema

-- G --

genome Data on a Genome
genome-method Data on a Genome
genome-method Ranges on a Genome
genome-method UCSC Schema
genome-method Class "BrowserSession"
genome-method Class "UCSCSession"
genome<- Data on a Genome
genome<--method Data on a Genome
genome<--method Ranges on a Genome
genome<--method Class "BrowserSession"
genome<--method Class "UCSCSession"
genomeBrowsers Get available genome browsers
GenomicData Data on a Genome
GenomicRanges Ranges on a Genome
GenomicSelection Genomic data selection
getTable Querying UCSC Tables
getTable-method Querying UCSC Tables
GRangesForBSGenome GRanges for a Genome
GRangesForUCSCGenome GRanges for a Genome
GraphTrackLine-class Class "GraphTrackLine"

-- I --

import Importing objects
import-method Importing objects
import.bed Importing tracks
import.bed-method Importing tracks
import.bed15 Importing tracks
import.bed15-method Importing tracks
import.bedGraph Importing tracks
import.bedGraph-method Importing tracks
import.bw Importing tracks
import.bw-method Importing tracks
import.chain Chain objects
import.chain-method Chain objects
import.gff Importing tracks
import.gff-method Importing tracks
import.gff1 Importing tracks
import.gff1-method Importing tracks
import.gff2 Importing tracks
import.gff2-method Importing tracks
import.gff3 Importing tracks
import.gff3-method Importing tracks
import.ucsc Importing tracks
import.ucsc-method Importing tracks
import.wig Importing tracks
import.wig-method Importing tracks
initialize-method Class "UCSCData"
initialize-method Class "UCSCSession"

-- L --

liftOver Lift intervals between genome builds
liftOver-method Lift intervals between genome builds

-- N --

names-method Querying UCSC Tables
names<--method Querying UCSC Tables
nrow-method UCSC Schema

-- O --

offset-method Chain objects

-- 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"
RangedData-methods Data on a Genome
ranges-method Chain objects
RangesList-methods Ranges on a Genome
reversed Chain objects
reversed-method Chain objects

-- S --

score-method Chain objects
sequence<- Load a sequence
sequence<--methods Load a sequence
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

-- 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 Querying UCSC Tables
track-method Class "UCSCSession"
track<- Laying tracks
track<--method Laying tracks
track<--methods Laying tracks
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 Accessing track names
trackNames-methods Accessing track names
trackNames<- Accessing track names
trackNames<--method Accessing track names
trackNames<--methods Accessing track names

-- U --

UCSCData-class Class "UCSCData"
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"

-- V --

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

-- misc --

$-method Class "BrowserSession"
$<--method Class "BrowserSession"
[-method Class "UCSCTrackModes"
[<--method Class "UCSCTrackModes"
[[-method Class "BrowserSession"
[[<--method Class "BrowserSession"