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 become "out of limits" after restriction be kept?
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 obtained by removing the set of integers described by x 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)
  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 1.1.55 Index]