List of RleViews

Description

An extension of RangesList that holds only RleViews objects. Useful for storing coverage vectors over a set of spaces (e.g. chromosomes), each of which requires a separate RleViews object. As a Sequence, RleViewsList may be annotated with its universe identifier (e.g. a genome) in which all of its spaces exist.

Details

For more information on methods available for RleViewsList objects consult the man pages for RangesList and Views-utils.

Constructor

RleViewsList(..., rleList, rangesList, universe = NULL): Either ... or the rleList/rangesList couplet provide the RleViews for the list. If ... is provided, each of these arguments must be RleViews objects. Alternatively, rleList and rangesList accept Rle and Ranges objects respectively that are meshed together for form the RleViewsList. The universe is specified by the universe parameter, which should be a single string or NULL, to leave unspecified.

Views(subject, start=NULL, end=NULL, width=NULL, names=NULL): Same as RleViewsList(rleList = subject, rangesList = start).

Coercion

In the code snippets below, from is an RleViewsList object:

as(from, "IRangesList"): Creates a CompressedIRangesList object containing the view locations in from.

as(from, "CompressedIRangesList"): Creates a CompressedIRangesList object containing the view locations in from.

as(from, "SimpleIRangesList"): Creates a SimpleIRangesList object containing the view locations in from.

Author(s)

P. Aboyoun

See Also

RangesList-class, Views-utils

Examples

  ## Rle objects
  subject1 <- Rle(c(3L,2L,18L,0L), c(3,2,1,5))
  set.seed(0)
  subject2 <- Rle(c(0L,5L,2L,0L,3L), c(8,5,2,7,4))

  ## Views
  rleViews1 <- Views(subject1, 3:0, 5:8)
  rleViews2 <- Views(subject2, subject2 > 0) 

  ## RleList and RangesList objects
  rleList <- RleList(subject1, subject2)
  rangesList <- IRangesList(IRanges(3:0, 5:8), IRanges(subject2 > 0))

  ## methods for construction
  method1 <- RleViewsList(rleViews1, rleViews2)
  method2 <- RleViewsList(rleList = rleList, rangesList = rangesList)
  identical(method1, method2)

  ## calculation over the views
  viewSums(method1)