UCSCFile objects
These functions support the import and export of tracks emucscded
within the UCSC track line metaformat, whereby multiple tracks may be
concatenated within a single file, along with metadata mostly oriented
towards visualization. Any UCSCData object is
automatically exported in this format, if the targeted format is known
to be compatible. The BED and WIG import methods check for a track
line, and delegate to these functions if one is found. Thus, calling
this API directly is only necessary when importing embedded GFF
(rare), or when one wants to create the track line during the export
process.
## S4 method for signature 'UCSCFile,ANY,ANY'
import(con, format, text,
subformat = "auto", drop = FALSE,
genome = NA, ...)
import.ucsc(con, ...)
## S4 method for signature 'ANY,UCSCFile,ANY'
export(object, con, format, ...)
## S4 method for signature 'GenomicRanges,UCSCFile,ANY'
export(object, con, format, ...)
## S4 method for signature 'GenomicRangesList,UCSCFile,ANY'
export(object, con, format,
append = FALSE, index = FALSE, ...)
## S4 method for signature 'UCSCData,UCSCFile,ANY'
export(object, con, format,
subformat = "auto", append = FALSE, index = FALSE, ...)
export.ucsc(object, con, ...)con |
A path, URL, connection or |
object |
The object to export, should be a |
format |
If not missing, should be “ucsc”. |
text |
If |
subformat |
The file format to use for the actual features,
between the track lines. Must be a text-based format that is
compatible with track lines (most are). If an |
genome |
The identifier of a genome, or |
drop |
If |
append |
If |
index |
If |
... |
Should either specify track line parameters or arguments to pass down to the import and export routine for the subformat. |
The UCSC track line permits the storage of multiple tracks in a single
file by separating them with a so-called “track line”, a line
belonging with the word “track” and containing
various key=value pairs encoding metadata, most related to
visualization. The standard fields in a track depend on the type of
track being annotated. See TrackLine and its
derivatives for how these lines are represented in R. The
class UCSCData is an extension
of GRanges with a formal slot for a TrackLine.
Each GRanges in the returned GenomicRangesList has the
track line stored in its metadata, under the trackLine key.
For each track object to be exported, if the object is not a
UCSCData, and there is no trackLine element in the
metadata, then a new track line needs to be generated. This happens
through the coercion of object to UCSCData. The track line
is initialized to have the appropriate type parameter for the
subformat, and the required name parameter is taken from the
name of the track in the input list (if any). Otherwise, the default
is simply “R Track”. The db parameter (specific to BED
track lines) is taken as genome(object) if not
NA. Additional arguments passed to the export routines
override parameters in the provided track line.
If the subformat is either WIG or BEDGraph, and the features are stranded, a separate track will be output in the file for each strand. Neither of those formats encodes the strand and disallow overlapping features (which might occur upon destranding).
A GenomicRangesList unless drop is TRUE
and there is only a single track in the file. In that case, the first and
only object is extracted from the list and returned.
The structure of that object depends on the format of the
data. The GenomicRangesList contains UCSCData objects.
The UCSCFile class extends RTLFile and is a
formal represention of a resource in the UCSC format.
To cast a path, URL or connection to a UCSCFile, pass it to
the UCSCFile constructor.
Michael Lawrence
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