UCSCData-class: Class "UCSCData"

In rtracklayer: R interface to genome annotation files and the UCSC genome browser

Description

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

Slots

trackLine:

Object of class "TrackLine" holding track metadata.

Methods

export.bed(object, con, variant = c("base", "bedGraph", "bed15"), color, trackLine = TRUE, ...)

Exports the track and its track line (if trackLine is TRUE) to con in the Browser Extended Display (BED) format. The arguments in ... are passed to export.ucsc.

export.bed15(object, con, expNames = NULL, ...)

Exports the track and its track line (if trackLine is TRUE) to con in the Bed15 format. The data is taken from the columns named in expNames, which defaults to the expNames in the track line, if any, otherwise all column names. The arguments in ... are passed to export.ucsc.

export.gff(object)

Exports the track and its track line (as a comment) to con in the General Feature Format (GFF).

export.ucsc(object, con, subformat, ...)

Exports the track and its track line to con in the UCSC meta-format.

as(object, "UCSCData")

Constructs a UCSCData from a GRanges instance, by adding a default track line and ensuring that the sequence/chromosome names are compliant with UCSC conventions. If there is a numeric score, the track line type is either "bedGraph" or "wig", depending on the feature density. Otherwise, "bed" is chosen.

Author(s)

Michael Lawrence

See Also

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

rtracklayer documentation built on Nov. 8, 2020, 6:50 p.m.