ucscTrackSet-class {rtracklayer}R Documentation

Class "ucscTrackSet"

Description

Each track in UCSC has an associated ucscTrackLine that contains metadata on the track.

Objects from the Class

Objects can be created by calls of the form new("ucscTrackSet", assayData, phenoData, featureData, experimentData, annotation, ...). See trackSet for more details.

Slots

trackLine:
Object of class "ucscTrackLine" holding track metadata.
genome:
Object of class "character" identifying the genome of this track, e.g. "hg18".
assayData:
Object of class "AssayData" holding the experimental measurements under dataVals.
phenoData:
Object of class "AnnotatedDataFrame" holding the experimental design matrix.
featureData:
Object of class "AnnotatedDataFrame" holding feature information, generally including columns chrom (chromosome), start (start position), end (end position) and strand (strand on the DNA: "+", "-", or NA).
experimentData:
Object of class "MIAME" holding experimental metadata.
annotation:
Object of class "character" referring to the annotation dataset.
.__classVersion__:
Object of class "Versions" holding version information.

Extends

Class "trackSet", directly. Class "eSet", by class "trackSet", distance 2. Class "VersionedBiobase", by class "trackSet", distance 3. Class "Versioned", by class "trackSet", distance 4.

Methods

export.bed(object, con, wig = FALSE, trackLine = !wig)
Exports the track and its track line (if trackLine is TRUE) to con in the Browser Extended Display (BED) format.
export.gff(object)
Exports the track and its track line (as a comment) to con in the General Feature Format (GFF).
export.ucsc(object)
Exports the track and its track line to con in the UCSC meta-format.

Author(s)

Michael Lawrence

See Also

import and export for reading and writing tracks to and from connections (files), respectively.


[Package rtracklayer version 1.2.2 Index]