trackSet-methods {rtracklayer}R Documentation

Get a trackSet

Description

Methods for getting a trackSet.

Usage

trackSet(object, ...)

Arguments

object An object from which to obtain a trackSet.
... Arguments passed on to methods.

Methods

The following methods are defined by rtracklayer.

object = "AnnotatedDataFrame"
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.
object = "data.frame"
trackSet(object, dataVals = NULL, ...): coerces object to AnnotatedDataFrame and delegates to it.
object = "IRanges"
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.
object = "character"
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.
object = "ucscSession"
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.
object = "argoSession"
trackSet(object, name, segment = genomeSegment(object)): Get a track from the session by its name.

See Also

layTrack for loading a trackSet into a session.

Examples

## 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)

[Package rtracklayer version 1.2.2 Index]