IRanges (version 2.4.1)

GappedRanges-class: GappedRanges objects

Description

The GappedRanges class is a vector-like container for storing a set of "gapped ranges".

Constructor

No constructor function is provided for GappedRanges objects. The coercion methods described below can be used to create GappedRanges objects.

Coercion

as(from, "GappedRanges"): Turns a CompressedNormalIRangesList or CompressedIRangesList object into a GappedRanges object.

as(from, "RangesList"): Turns a GappedRanges object into a RangesList object (more precisely the result will be a CompressedNormalIRangesList object).

Accessor methods

In the code snippets below, x is a GappedRanges object.

length(x): Returns the number of "gapped ranges" in x.

start(x), end(x): Returns an integer vector of length length(x) containing the start and end (respectively) of each "gapped range" in x. See Details section above for the exact definitions of the start and end of a "gapped range".

width(x): Defined as end(x) - start(x) + 1L.

ngap(x): Returns an integer vector of length length(x) containing the number of gaps for each "gapped range" in x. Equivalent to elementLengths(x) - 1L.

names(x): NULL or a character vector of length length(x).

Subsetting and related operations

In the code snippets below, x is a GappedRanges object.

x[i]: Returns a new GappedRanges object made of the selected "gapped ranges". i can be a numeric, character or logical vector, or any of the types supported by the [ method for CompressedNormalIRangesList objects.

x[[i]]: Returns the NormalIRanges object representing the i-th element in x. Equivalent to as(from, "RangesList")[[i]]. i can be a single numeric value or a single character string.

elemenType(x): Returns the type of x[[i]] as a single string (always "NormalIRanges"). Note that the semantic of the [[ method for GappedRanges objects is different from the semantic of the method for Ranges objects (the latter returns an integer vector).

elementLengths(x): Semantically equivalent to

sapply(seq_len(length(x)), function(i) length(x[[i]]))

but much faster. Note that the semantic of the elementLengths method for GappedRanges objects is different from the semantic of the method for Ranges objects (the latter returns the width of the Ranges object).

Combining and related operations

In the code snippets below, x is a GappedRanges object.

c(x, ...): Combine x and the GappedRanges objects in ... together. The result is an object of the same class as x.

Details

A "gapped range" is conceptually the union of 1 or more non-overlapping (and non-empty) ranges ordered from left to right. More precisely, a "gapped range" can be represented by a normal IRanges object of length >= 1. In particular normality here ensures that the individual ranges are non-empty and are separated by non-empty gaps. The start of a "gapped range" is the start of its first range. The end of a "gapped range" is the end of its last range. If we ignore the gaps, then a GappedRanges object can be seen as a Ranges object.

See Also

Ranges-class, CompressedNormalIRangesList-class

Examples

  ## The 3 following IRanges objects are normal. Each of them will be
  ## stored as a "gapped range" in the GappedRanges object 'gr'.
  ir1 <- IRanges(start=c(11, 21, 23), end=c(15, 21, 30))
  ir2 <- IRanges(start=-2, end=15)
  ir3 <- IRanges(start=c(-2, 21), end=c(10, 22))
  irl <- IRangesList(ir1, ir2, ir3)

  gr <- as(irl, "GappedRanges")
  gr

  length(gr)
  start(gr)
  end(gr)
  width(gr)
  ngap(gr)
  gr[-1]
  gr[ngap(gr) >= 1]
  gr[[1]]
  as.integer(gr[[1]])
  gr[[2]]
  as.integer(gr[[2]])
  as(gr, "RangesList")
  start(as(gr, "RangesList"))  # not the same as 'start(gr)'