R: Accessing sequence information

seqinfo {GenomicRanges}

R Documentation

Accessing sequence information

Description

A set of generic functions for getting/setting sequence information from/on an object.

Usage

seqinfo(x)
seqinfo(x, new2old=NULL, force=FALSE) <- value

seqnames(x)
seqnames(x) <- value

seqlevels(x)
seqlevels(x, force=FALSE) <- value

seqlengths(x)
seqlengths(x) <- value

isCircular(x)
isCircular(x) <- value

genome(x)
genome(x) <- value

seqnameStyle(x)
seqnameStyle(x) <- value

Arguments

`x`	The object from/on which to get/set the sequence information.
`new2old`	The `new2old` argument allows the user to rename, drop, add and/or reorder the "sequence levels" in `x`. `new2old` can be `NULL` or an integer vector with one element per row in Seqinfo object `value` (i.e. `new2old` and `value` must have the same length) describing how the "new" sequence levels should be mapped to the "old" sequence levels, that is, how the rows in `value` should be mapped to the rows in `seqinfo(x)`. The values in `new2old` must be >= 1 and <= `length(seqinfo(x))`. `NA`s are allowed and indicate sequence levels that are being added. Old sequence levels that are not represented in `new2old` will be dropped, but this will fail if those levels are in use (e.g. if `x` is a GRanges object with ranges defined on those sequence levels) unless `force=TRUE` is used (see below). If `new2old=NULL`, then sequence levels can only be added to the existing ones, that is, `value` must have at least as many rows as `seqinfo(x)` (i.e. `length(values) >= length(seqinfo(x))`) and also `seqlevels(values)[seq_len(length(seqlevels(x)))]` must be identical to `seqlevels(x)`.
`force`	Force dropping sequence levels currently in use. This is achieved by dropping the elements in `x` where those levels are used (hence typically reducing the length of `x`).
`value`	Typically a Seqinfo object for the `seqinfo` setter. Either a named or unnamed character vector for the `seqlevels` setter. A vector containing the sequence information to store for the other setters.

Details

Various classes implement methods for those generic functions.

The Seqinfo class plays a central role for those generics because:

It has methods for all those generics (except seqinfo). That is, the seqnames, seqlevels, seqlengths, isCircular, genome and seqnameStyle getters and setters are defined for Seqinfo objects.
For classes that implement it, the seqinfo getter should return a Seqinfo object.
Default seqlevels, seqlengths, isCircular, genome, and seqnameStyle getters and setters are provided. By default, seqlevels(x) does seqlevels(seqinfo(x)), seqlengths(x) does seqlengths(seqinfo(x)), isCircular(x) does isCircular(seqinfo(x)), genome(x) does genome(seqinfo(x)), and seqnameStyle(x) does seqnameStyle(seqinfo(x)). So any class with a seqinfo getter will have all the above getters work out-of-the-box. If, in addition, the class defines a seqinfo setter, then all the corresponding setters will also work out-of-the-box.

See the GRanges, GRangesList, GappedAlignments, and GappedAlignmentPairs classes for examples of classes that define the seqinfo getter and setter (those 4 classes are defined in the GenomicRanges package).

See the TranscriptDb class (defined in the GenomicFeatures package) for an example of a class that defines only the seqinfo getter (no setter).

The GenomicRanges package defines seqinfo and seqinfo<- methods for these low-level IRanges data structures: List, RangesList and RangedData. Those objects do not have the means to formally store sequence information. Thus, the wrappers simply store the Seqinfo object within metadata(x). Initially, the metadata is empty, so there is some effort to generate a reasonable default Seqinfo. The names of any List are taken as the seqnames, and the universe of RangesList or RangedData is taken as the genome.

Note

The full list of methods defined for a given generic can be seen with e.g. showMethods("seqinfo") or showMethods("seqnames") (for the getters), and showMethods("seqinfo<-") or showMethods("seqnames<-") (for the setters aka replacement methods). Please be aware that this shows only methods defined in packages that are currently attached.

Examples

  showMethods("seqinfo")
  showMethods("seqinfo<-")

  showMethods("seqnames")
  showMethods("seqnames<-")

  if (interactive())
    ?`GRanges-class`

[Package GenomicRanges version 1.12.1 Index]