Sequence-class {IRanges} | R Documentation

## Sequence objects

### Description

The Sequence virtual class is a general container for storing a sequence i.e. an ordered set of elements. These containers come in three types: XSequence, XRle [DEPRECATED], and Rle.

The XSequence virtual class is a general container for storing an "external sequence". The following classes derive directly from the XSequence class.

The XRaw class is a container for storing an external sequence of bytes (stored as char values at the C level).

The XInteger class is a container for storing an external sequence of integer values (stored as int values at the C level).

The XNumeric class is a container for storing an external sequence of numeric values (stored as double values at the C level).

Also the XString class from the Biostrings package

The XRle [DEPRECATED – use Rle] virtual class is a general container for storing an "external sequence" that is stored in a run-length encoding format. The following classes derive directly from the XRle class.

The XRleInteger [DEPRECATED – use Rle] class is a container for storing an external run-length encoding of integers (stored as int values at the C level).

The purpose of the X* containers is to provide a "pass by address" semantic and also to avoid the overhead of copying the sequence data when a linear subsequence needs to be extracted.

For information on the Rle class, type `help(Rle)`.

### Combining

In the code snippets below, `x` is a Sequence object.

  `c(x, ...)`: Combine `x` and the Sequence objects in `...` together. Any object in `...` must belong to the same class as `x`, or to one of its subclasses, or must be `NULL`. The result is an object of the same class as `x`. NOTE: Only works for XRaw (and derived) objects for now.

### Subsetting

In the code snippets below, `x` is a Sequence object.

  `subseq(x, start=NA, end=NA, width=NA)`: Extract the subsequence from `x` specified by `start`, `end` and `width`. The supplied start/end/width values are solved by a call to `solveUserSEW(length(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).

  A note about performance: `subseq` does NOT copy the sequence data of an XSequence object. Hence it's very efficient and is therefore the recommended way to extract a linear subsequence (i.e. a set of consecutive elements) from an XSequence object. For example, extracting a 100Mb subsequence from Human chromosome 1 (a 250Mb DNAString object) with `subseq` is (almost) instantaneous and has (almost) no memory footprint (the cost in time and memory does not depend on the length of the original sequence or on the length of the subsequence to extract).

  `subseq(x, start=NA, end=NA, width=NA) <- value`: Replace the subsequence specified on the left (i.e. the subsequence in `x` specified by `start`, `end` and `width`) by `value`. `value` must belong to the same class as `x`, or to one of its subclasses, or must be `NULL`. This replacement method can modify the length of `x`, depending on how the length of the left subsequence compares to the length of `value`. It can be used for inserting elements in `x` (specify an empty left subsequence for this) or deleting elements from `x` (use a `NULL` rigth value for this). Unlike the extraction method above, this replacement method always copies the sequence data of `x` (even for XSequence objects). NOTE: Only works for XRaw (and derived) objects for now.
  `x[i, drop=TRUE]`: Return a new Sequence object made of the selected elements (subscript `i` must be an NA-free numeric vector specifying the positions of the elements to select). The `drop` argument specifies whether or not to coerce the returned sequence to a standard vector.
  `rep(x, times)`: Return a new Sequence object made of the repeated elements.

### See Also

Rle-class, Views-class, `solveUserSEW`, DNAString-class

### Examples

      ## ---------------------------------------------------------------------
      ## A. XRaw OBJECTS
      ## ---------------------------------------------------------------------

      x1 <- XRaw(4)  # values are not initialized
      x1
      x2 <- as(c(255, 255, 199), "XRaw")
      x2
      y <- c(x1, x2, NULL, x1)  # NULLs are ignored
      y
      subseq(y, start=-4)
      subseq(y, start=-4) <- x2
      y

      ## ---------------------------------------------------------------------
      ## B. XInteger OBJECTS
      ## ---------------------------------------------------------------------

      x3 <- XInteger(12, val=c(-1:10))
      x3
      length(x3)

      ## Subsetting
      x4 <- XInteger(99999, val=sample(99, 99999, replace=TRUE) - 50)
      x4
      subseq(x4, start=10)
      subseq(x4, start=-10)
      subseq(x4, start=-20, end=-10)
      subseq(x4, start=10, width=5)
      subseq(x4, end=10, width=5)
      subseq(x4, end=10, width=0)

      x3[length(x3):1]
      x3[length(x3):1, drop=FALSE]

      x5 <- LETTERS
      subseq(x5, 8, 11) <- x5[11:8]  # swap 8<->11 and 9<->10 elements
      subseq(x5, start=1, width=0) <- c("xx", "yyy")  # insert 2 elements at the beginning
      subseq(x5, end=-1, width=0) <- letters[1:3]  # insert 3 elements at the end
      subseq(x5, end=-4, width=5) <- NULL  # remove 5 elements before the just added ones

[Package IRanges version 1.2.3 Index]