UCSCData-class {rtracklayer}R Documentation

Class "UCSCData"

Description

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

Slots

trackLine:
Object of class "TrackLine" 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.

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.
as(object, "UCSCData")
Constructs a UCSCData from a RangedData instance, by adding a default track line and ensuring that the sequence/chromosome names are compliant with UCSC conventions.

Author(s)

Michael Lawrence

See Also

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


[Package rtracklayer version 1.4.1 Index]