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 two types: XSequence and XRle.

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 virtual class is a general container for storing an "external sequence" that is stored in a run-time encoding format. The following classes derive directly from the XRle class.

The XRleInteger class is a container for storing an external run-length encoding of integers (stored as char values at the C level).

The purpose of these 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.

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).

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

Views-class, solveUserSEW, DNAString-class

Examples

  x1 <- XInteger(12, c(-1:10))
  x1
  length(x1)

  ## Subsetting
  x2 <- XInteger(99999, sample(99, 99999, replace=TRUE) - 50)
  x2
  subseq(x2, start=10)
  subseq(x2, start=-10)
  subseq(x2, start=-20, end=-10)
  subseq(x2, start=10, width=5)
  subseq(x2, end=10, width=5)
  subseq(x2, end=10, width=0)

  x1[length(x1):1]
  x1[length(x1):1, drop=FALSE]

[Package IRanges version 1.0.16 Index]