UCSCData-class: 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.
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.
See Also
import and export for reading and writing
tracks to and from connections (files), respectively.