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.
Methods
export.bed(object, con, variant = c("base", "bedGraph", "bed15"), color, trackLine = TRUE, ...)
-
Exports the track and its track line (if
trackLine
isTRUE
) tocon
in the Browser Extended Display (BED) format. The arguments in...
are passed toexport.ucsc
. export.bed15(object, con, expNames = NULL, ...)
-
Exports the track and its track line (if
trackLine
isTRUE
) tocon
in the Bed15 format. The data is taken from the columns named inexpNames
, which defaults to theexpNames
in the track line, if any, otherwise all column names. The arguments in...
are passed toexport.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 aGRanges
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.