XDoubleViews-class: The XDoubleViews class

In XVector: Foundation of external vector representation and manipulation in Bioconductor

Description

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

Details

An XDoubleViews object contains a set of views (start/end locations) on the same XDouble object called "the subject numeric vector" or simply "the subject". Each view is defined by its start and end locations: both are integers such that start <= end. An XDoubleViews object is in fact a particular case of a Views object (the XDoubleViews 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 XDoubleViews objects, and i can be a numeric or logical vector.

x[[i]]: Extract a view as an XDouble 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 XDouble 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 XDoubleViews object being compared are recycled as necessary.

e1 != e2: Equivalent to !(e1 == e2).

Author(s)

P. Aboyoun for the XIntegerViews* code, which was adapted to work over XDouble's by S. Lianoglou

See Also

view-summarization-methods, Views-class, XDouble-class, XIntegerViews-class

Examples

  ## One standard way to create an XDoubleViews object is to use
  ## the Views() constructor:
  subject <- as(rnorm(6), "XDouble")
  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:
  idx <- start(v4) < 1 | end(v4) > length(subject(v4))
  names(v4)[idx] <- "out of limits"

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

  ## It is an error to try to extract an "out of limits" view:
## Not run: 
  v4[[3]] # Error!

## End(Not run)

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

  ## Some fast view* functionalities:
  x <- rnorm(55)
  bounds <- IRanges(c(1, 11, 35, 20), width=c(5, 10, 15, 28))
  v <- Views(x, bounds)
  val <- viewMins(v)
  expect <- sapply(1:length(bounds), function(i) {
    min(x[start(bounds)[i]:end(bounds[i])])
  })
  stopifnot(all(val == expect))

XVector documentation built on Nov. 8, 2020, 5:19 p.m.