R Graphical Manual

Last data update: 2014.03.03

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BEDFile-class (Package: rtracklayer) : BEDFile objects

These functions support the import and export of the UCSC BED format and its variants, including BEDGraph.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: BED15File-class, BEDFile-class, BEDGraphFile-class, BEDPEFile-class, class:BED15File, class:BEDFile, class:BEDGraphFile
● 0 images

BamFile-methods (Package: rtracklayer) : Export to BAM Files

Methods for import and export of GAlignments or GAlignmentPairs objects from and to BAM files, represented as BamFile objects.

● Data Source: BioConductor
● Keywords:
● Alias: export,ANY,BamFile,ANY-method, export,GAlignmentPairs,BamFile,ANY-method, export,GAlignments,BamFile,ANY-method, import,BamFile,ANY,ANY-method
● 0 images

Bed15TrackLine-class (Package: rtracklayer) : Class "Bed15TrackLine"

A UCSC track line for graphical tracks.

● Data Source: BioConductor
● Keywords: classes
● Alias: Bed15TrackLine-class, coerce,Bed15TrackLine,character-method, coerce,character,Bed15TrackLine-method
● 0 images

BigWigFile-class (Package: rtracklayer) : BigWig Import and Export

These functions support the import and export of the UCSC BigWig format, a compressed, binary form of WIG/BEDGraph with a spatial index and precomputed summaries. These functions do not work on Windows.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: BWFile-class, BigWigFile-class, BigWigFileList-class, class:BWFile, class:BigWigFile, class:BigWigFileList
● 0 images

BigWigSelection-class (Package: rtracklayer) : Selection of ranges and columns

A BigWigSelection represents a query against a BigWig file, see import.bw. It is simply a RangedSelection that requires its colnames parameter to be "score", if non-empty, as that is the only column supported by BigWig.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: BigWigSelection-class
● 0 images

BrowserViewList-class (Package: rtracklayer) : Lists of BrowserView

A formal list of BrowserView objects. Extends and inherits all its methods from Vector. Usually generated by passing multiple ranges to the browserView function.

● Data Source: BioConductor
● Keywords: classes
● Alias: BrowserViewList-class
● 0 images

Chain-class (Package: rtracklayer) : Chain objects

A Chain object represents a UCSC chain alignment, typically imported from a chain file, and is essentially a list of ChainBlock objects. Each ChainBlock has a corresponding chromosome (its name in the list) and is a run-length encoded alignment, mapping a set of intervals on that chromosome to intervals on the same or other chromosomes.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: Chain-class, ChainBlock-class, ChainFile-class, class:Chain, class:ChainBlock, class:ChainFile
● 0 images

FastaFile-class (Package: rtracklayer) : FastaFile objects

These functions support the import and export of the Fasta sequence format, using the Biostrings package.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: FastaFile-class, class:FastaFile
● 0 images

GFFFile-class (Package: rtracklayer) : GFFFile objects

These functions support the import and export of the GFF format, of which there are three versions and several flavors.

● Data Source: BioConductor
● Keywords: classes, methods
● Alias: GFF1File-class, GFF2File-class, GFF3File-class, GFFFile-class, GTFFile-class, GVFFile-class, class:GFF1File, class:GFF2File, class:GFF3File, class:GFFFile, class:GTFFile, class:GVFFile
● 0 images

GRangesForUCSCGenome (Package: rtracklayer) :

These functions assist in the creation of Seqinfo or GRanges for a genome.

● Data Source: BioConductor
● Keywords:
● Alias: GRangesForBSGenome, GRangesForUCSCGenome, SeqinfoForBSGenome, SeqinfoForUCSCGenome
● 0 images