Seqinfo-class {GenomicRanges}R Documentation

Seqinfo objects

Description

A Seqinfo object is a data.frame-like object that contains basic information about a set of genomic sequences. Currently only the length and circularity flag of each sequence is stored but more information might be added in the future.

Details

Typically Seqinfo objects are not used directly but are part of higher level objects.

Constructor

Seqinfo(seqnames, seqlengths=NA, isCircular=NA): Creates a Seqinfo object.

Accessor methods

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

length(x): Gets the number of sequences in x.
seqnames(x), seqnames(x) <- value: Gets/sets the names of the sequences in x.
names(x), names(x) <- value: Same as seqnames(x) and seqnames(x) <- value.
seqlengths(x), seqlengths(x) <- value: Gets/sets the lengths of the sequences in x.
isCircular(x), isCircular(x) <- value: Gets/sets the circularity flags of the sequences in x.
isCircularWithKnownLength(x): Formally defined as (isCircular(x) %in% TRUE) & !is.na(seqlengths(x)).

Coercion

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

as.data.frame(x): Turns x into a data frame.

Author(s)

H. Pages

Examples

  ## Coming soon...

[Package GenomicRanges version 1.2.3 Index]