seqnames {GenomicRanges}R Documentation

Accessing the sequence names and lengths stored in an object

Description

The seqnames and seqlengths generics are meant as accessors for the sequence names and lengths stored in an object, respectively.

Usage

  seqnames(x)
  seqlengths(x)

Arguments

x The object from which to access the sequence information.

Details

Various classes provide seqnames and seqlengths methods for getting or setting the sequence names and lengths of an object of the class, respectively.

See for example ?`seqnames,GRanges-method` for the GRanges class and ?`seqnames,GRangesList-method` for the GRangesList class, both classes being defined in the GenomicRanges package.

For more examples see ?`seqnames,BSgenome-method` for the BSgenome class defined in the BSgenome package and ?`seqnames,TranscriptDb-method` for the TranscriptDb class defined in the GenomicFeatures package (you might need to install and load these packages first).

The full list can be seen with showMethods("seqnames") and showMethods("seqlengths") (for the get methods) and showMethods("seqnames<-") and showMethods("seqlengths<-") (for the replacement methods).

See Also

seqnames,GRanges-method, seqnames,GRangesList-method, seqnames,BSgenome-method seqnames,TranscriptDb-method

Examples

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

  showMethods("seqlengths")
  showMethods("seqlengths<-")

  ?`seqnames,GRanges-method`

[Package GenomicRanges version 1.0.9 Index]