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)