genomeSegment-methods {rtracklayer}R Documentation

Accessing a segment of a genome

Description

Methods for creating, getting or setting a genomeSegment.

Methods

The following methods are defined by rtracklayer.

object = "character"
genomeSegment(object, chrom = character(0), start = character(0), end = character(0), segment = genomeSegment()): Create a genomeSegment instance with the same slot values as segment, except where overriden by one of the other parameters, which all correspond to slots in genomeSegment. Note that object corresponds to the genome slot.
object = "missing"
genomeSegment(object, genome = character(0), chrom = character(0), start = character(0), end = character(0), segment = new("genomeSegment")): Similar to above, except object is omitted and genome is an explicit parameter.
object = "trackSet"
Get the segment spanned by a track.
object = "trackSets"
Get the union (including gaps) of spans for all tracks.
object = "browserSession"
Get the current segment (i.e. segment displayed by active view or default segment).
object = "ucscSession"
Get the last accessed segment.
object = "ucscView" or "argoView"
genomeSegment(object): Get the segment displayed by the view.

genomeSegment(object) <- value: Set the segment displayed by the the view.

object = "IRanges"
Obtain the genome segment that spans the range of the IRanges object.

Examples

  ## Create a genome segment for genome "hg18", chromosome 22
  genomeSegment("hg18", "chr22")
  ## Explicitly specify parameters
  segment <- genomeSegment(genome = "hg18", chrom = "chr22", start = 150000)
  ## Add an 'end' value
  genomeSegment(end = 200000, segment = segment)

[Package rtracklayer version 1.2.2 Index]