XIntegerViews-class {IRanges}R Documentation

The XIntegerViews class

Description

The XIntegerViews class is the basic container for storing a set of views (start/end locations) on the same XInteger object.

Details

An XIntegerViews object contains a set of views (start/end locations) on the same XInteger object called "the subject integer vector" or simply "the subject". Each view is defined by its start and end locations: both are integers such that start <= end. An XIntegerViews object is in fact a particular case of a Views object (the XIntegerViews class contains the Views class) so it can be manipulated in a similar manner: see ?Views for more information. Note that two views can overlap and that a view can be "out of limits" i.e. it can start before the first element of the subject or/and end after its last element.

Other methods

In the code snippets below, x, object, e1 and e2 are XIntegerViews objects, and i can be a numeric or logical vector.

x[[i]]: Extract a view as an XInteger object. i must be a single numeric value (a numeric vector of length 1). Can't be used for extracting a view that is "out of limits" (raise an error). The returned object has the same XInteger subtype as subject(x).
e1 == e2: A vector of logicals indicating the result of the view by view comparison. The views in the shorter of the two XIntegerViews object being compared are recycled as necessary.
e1 != e2: Equivalent to !(e1 == e2).

Author(s)

P. Aboyoun

See Also

Views-class, XInteger-class, Views-utils

Examples

  ## One standard way to create an XIntegerViews object is to use
  ## the Views() constructor:
  subject <- as(c(45, 67, 84, 67, 45, 78), "XInteger")
  v4 <- Views(subject, start=3:0, end=5:8)
  v4
  subject(v4)
  length(v4)
  start(v4)
  end(v4)
  width(v4)

  ## Attach a comment to views #3 and #4:
  names(v4)[3:4] <- "out of limits"
  names(v4)

  ## A more programatical way to "tag" the "out of limits" views:
  names(v4)[start(v4) < 1 | length(subject(v4)) < end(v4)] <- "out of limits"
  ## or just:
  names(v4)[length(subject(v4)) < width(v4)] <- "out of limits"

  ## Extract a view as an XInteger object:
  v4[[2]]

  ## It is an error to try to extract an "out of limits" view:
  #v4[[3]] # Error!

  ## Here the first view doesn't even overlap with the subject:
  subject <- as(c(97, 97, 97, 45, 45, 98), "XInteger")
  Views(subject, start=-3:4, end=-3:4 + c(3:6, 6:3))

[Package IRanges version 1.6.16 Index]