| trackSet-methods {rtracklayer} | R Documentation |
Methods for getting a trackSet.
trackSet(object, ...)
object |
An object from which to obtain a trackSet. |
... |
Arguments passed on to methods. |
trackSet(object, dataVals = NULL, ...):
A constructor that sets object directly as the
featureData slot and dataVals into the
dataVals slot, if non-NULL. The arguments in
... should correspond to slots in the trackSet class.
trackSet(object, dataVals = NULL, ...): coerces
object to AnnotatedDataFrame and delegates to it.
trackSet(object, chrom, strand = NA, dataVals = NULL, ...):
Constructor that takes the start and end of each feature from
object. The chromsome, strand, data values and other slots
are specified by chrom, strand, dataVals and
..., respectively.
trackSet(object, start = 1, end = start + span - 1, strand = NA,
span = 1, dataVals = NULL, breaks = NULL, ...): a constructor
that takes object to be the chromosome
values. start, end, strand and
dataVals specify the starts, ends, strands and data
values, respectively, of the features. span, if given,
should be a scalar integer indicating widths of the features
If end is specified with span, it must be length one
and then the region from start to end is broken up
into features of width span. If breaks is specified,
span must be omitted and start and end must
be scalars. Then the features are formed by breaking the region
from start to end at the positions specified in
breaks. Way too complicated for its own good.
trackSet(object, name, segment = genomeSegment(object), format =
"bed", table = NULL):
Get a track from the session by its name in format
format. Some built-in tracks have multiple series, each
identified by a table name.
trackSet(object, name, segment = genomeSegment(object)):
Get a track from the session by its name.
layTrack for loading a trackSet into a session.
## Not run:
session <- browseGenome()
track <- import(system.file("tests", "v1.gff", package = "rtracklayer"))
session <- layTrack(session, track, "My Track", format = "gff1", view = TRUE)
track <- trackSet(session, name = "My Track")
## End(Not run)