IRanges-utils {IRanges} | R Documentation

## IRanges utility functions

### Description

Utility functions for creating or modifying IRanges objects.

### Usage

      ## Create an IRanges instance:
      successiveIRanges(width, gapwidth=0, from=1)

      ## Turn a logical vector into a set of ranges:
      whichAsIRanges(x)

      ## Modify an IRanges object (endomorphisms):
      shift(x, shift, use.names=TRUE)
      restrict(x, start=NA, end=NA, keep.all.ranges=FALSE, use.names=TRUE)
      narrow(x, start=NA, end=NA, width=NA, use.names=TRUE)
      threebands(x, start=NA, end=NA, width=NA)
      reduce(x, with.inframe.attrib=FALSE)
      gaps(x, start=NA, end=NA)

      ## Other utilities
      ## S4 method for signature 'Ranges':
      reflect(x, bounds)
      ## S4 method for signature 'Ranges':
      flank(x, width, start = TRUE, both = FALSE)
      ## S4 method for signature 'Ranges':
      range(x, ..., na.rm = FALSE)

      ## Coercion:
      asNormalIRanges(x, force=TRUE)

### Arguments

`width` | For `successiveIRanges`, must be a vector of non-negative integers (with no NAs) specifying the widths of the ranges to create. For `narrow` and `threebands`, a vector of integers, eventually with NAs. See the SEW (Start/End/Width) interface for the details (`?solveUserSEW`). For `flank`, the width of the flanking regions. Note that if `both` is `TRUE`, this is effectively doubled. Recycled as necessary so that each element corresponds to a range in `x`.
`gapwidth` | A single integer or an integer vector with one less element than the `width` vector specifying the widths of the gaps separating one range from the next one.
`from` | A single integer specifying the starting position of the first range.
`x` | A logical vector for `whichAsIRanges`. An IRanges object for `shift`, `restrict`, `narrow`, `threebands`, `reduce`, `gaps` and `asNormalIRanges`.
`shift` | A single integer.
`use.names` | `TRUE` or `FALSE`. Should names be preserved?
`start, end` | A single integer or `NA` for all functions except `narrow` and `threebands`. For `narrow` and `threebands`, the supplied `start` and `end` arguments must be vectors of integers, eventually with NAs, that contain coordinates relative to the current ranges. See the Details section below. For `flank`, `start` is a logical indicating whether `x` should be flanked at the start (`TRUE`) or the end (`FALSE`). Recycled as necessary so that each element corresponds to a range in `x`.
`keep.all.ranges` | `TRUE` or `FALSE`. Should ranges that don't overlap with the interval specified by `start` and `end` be kept? Note that "don't overlap" means that they end strictly before `start - 1` or start strictly after `end + 1`. Ranges that end at `start - 1` or start at `end + 1` are always kept and their width is set to zero in the returned IRanges object.
`with.inframe.attrib` | `TRUE` or `FALSE`. For internal use.
`bounds` | An IRanges object to serve as the reference bounds for the reflection, see below.
`both` | If `TRUE`, extends the flanking region `width` positions into the range. The resulting range thus straddles the end point, with `width` positions on either side.
`...` | Additional `Ranges` to consider.
`na.rm` | Ignored
`force` | `TRUE` or `FALSE`. Should `x` be turned into a NormalIRanges object even if `isNormal(x)` is `FALSE`?

### Details

`successiveIRanges` returns an IRanges object containing the ranges on `subject` that have the widths specified in the `width` vector and are separated by the gaps specified in `gapwidth`. The first range starts at position `from`.

`whichAsIRanges` returns an IRanges object containing all of the ranges where `x` is `TRUE`.

`shift` shifts all the ranges in `x`.

`restrict` restricts the ranges in `x` to the interval specified by the `start` and `end` arguments.

`narrow` narrows the ranges in `x` i.e. each range in the returned IRanges object is a subrange of the corresponding range in `x`. The supplied start/end/width values are solved by a call to `solveUserSEW(width(x), start=start, end=end, width=width)` and therefore must be compliant with the rules of the SEW (Start/End/Width) interface (see `?solveUserSEW` for the details). Then each subrange is derived from the original range according to the solved start/end/width values for this range. Note that those solved values are interpreted relatively to the original range.

`threebands` extends the capability of `narrow` by returning the 3 ranges objects associated to the narrowing operation. The returned value `y` is a list of 3 ranges objects named `"left"`, `"middle"` and `"right"`. The middle component is obtained by calling `narrow` with the same arguments (except that names are dropped). The left and right components are also instances of the same class as `x` and they contain what has been removed on the left and right sides (respectively) of the original ranges during the narrowing.

Note that original object `x` can be reconstructed from the left and right bands with `punion(y$left, y$right, fill.gap=TRUE)`.

`reduce` first orders the ranges in `x` from left to right, then merges the overlapping or adjacent ones.

`gaps` returns the normal IRanges object describing the set of integers that remain after the set of integers described by `x` has been removed from the interval specified by the `start` and `end` arguments.

`reflect` "reflects" or reverses each range in `x` relative to the corresponding range in `bounds`, which is recycled as necessary. Reflection preserves the width of a range, but shifts it such the distance from the left bound to the start of the range becomes the distance from the end of the range to the right bound. This is illustrated below, where `x` represents a range in `x` and `[` and `]` indicate the bounds:

        [..xxx.....]
        becomes
        [.....xxx..]

`flank` generates flanking ranges for each range in `x`. If `start` is `TRUE` for a given range, the flanking occurs at the start, otherwise the end. The widths of the flanks are given by the `width` parameter. The widths can be negative, in which case the flanking region is reversed so that it represents a prefix or suffix of the range in `x`. The `flank` operation is illustrated below for a call of the form `flank(x, 3, TRUE)`, where `x` indicates a range in `x` and `-` indicates the resulting flanking region:

        ---xxxxxxx

If `start` were `FALSE`:

           xxxxxxx---

For negative width, i.e. `flank(x, -3, FALSE)`, where `*` indicates the overlap between `x` and the result:

           xxxx***

If `both` is `TRUE`, then, for all ranges in `x`, the flanking regions are extended into (or out of, if width is negative) the range, so that the result straddles the given endpoint and has twice the width given by `width`. This is illustrated below for `flank(x, 3, both=TRUE)`:

        ---***xxxx

`range` returns an `IRanges` instance with a single range, from the minimum start to the maximum end in the combined ranges of `x` and the arguments in `...`.

If `force=TRUE` (the default), then `asNormalIRanges` will turn `x` into a NormalIRanges instance by reordering and reducing the set of ranges if necessary (i.e. only if `isNormal(x)` is `FALSE`, otherwise the set of ranges will be untouched). If `force=FALSE`, then `asNormalIRanges` will turn `x` into a NormalIRanges instance only if `isNormal(x)` is `TRUE`, otherwise it will raise an error. Note that when `force=FALSE`, the returned object is guaranteed to contain exactly the same set of ranges than `x`. `as(x, "NormalIRanges")` is equivalent to `asNormalIRanges(x, force=TRUE)`.

### Author(s)

H. Pages and M. Lawrence

### See Also

Ranges-class, IRanges-class, IRanges-setops, `solveUserSEW`, `successiveViews`

### Examples

      vec <- as.integer(c(19, 5, 0, 8, 5))
      whichAsIRanges(vec >= 5)
      x <- successiveIRanges(vec)
      x
      shift(x, -3)
      restrict(x, start=12, end=34)
      restrict(x, start=20)
      restrict(x, start=21)
      restrict(x, start=21, keep.all.ranges=TRUE)

      y <- x[width(x) != 0]
      narrow(y, start=4, end=-2)
      narrow(y, start=-4, end=-2)
      narrow(y, end=5, width=3)
      narrow(y, start = c(3, 4, 2, 3), end = c(12, 5, 7, 4))

      z <- threebands(y, start=4, end=-2)
      y0 <- punion(z$left, z$right, fill.gap=TRUE)
      identical(y, y0)  # TRUE
      threebands(y, start=-5)

      x <- IRanges(start=c(-2L, 6L, 9L, -4L, 1L, 0L, -6L, 10L),
                   width=c( 5L, 0L, 6L,  1L, 4L, 3L,  2L,  3L))
      reduce(x)
      gaps(x)
      gaps(x, start=-6, end=20)  # Regions of the -6:20 range that are not masked by 'x'.

      ir1 <- IRanges(c(2,5,1), c(3,7,3))

      bounds <- IRanges(c(0, 5, 3), c(10, 6, 9))
      reflect(ir1, bounds)

      flank(ir1, 2)
      flank(ir1, 2, FALSE)
      flank(ir1, 2, c(FALSE, TRUE, FALSE))
      flank(ir1, c(2, -2, 2))
      flank(ir1, 2, both = TRUE)
      flank(ir1, 2, FALSE, TRUE)
      flank(ir1, -2, FALSE, TRUE)

      asNormalIRanges(x)   # 3 ranges ordered from left to right and separated by
                           # gaps of width >= 1.

      ## More on normality:
      example(`IRanges-class`)
      isNormal(x16)                        # FALSE
      if (interactive())
          x16 <- asNormalIRanges(x16)      # Error!
      whichFirstNotNormal(x16)             # 57
      isNormal(x16[1:56])                  # TRUE
      xx <- asNormalIRanges(x16[1:56])
      class(xx)
      max(xx)
      min(xx)

[Package IRanges version 1.2.3 Index]