XStringSet-class {Biostrings}R Documentation

BStringSet, DNAStringSet, RNAStringSet and AAStringSet objects

Description

The BStringSet class is a container for storing a set of BString objects and for making its manipulation easy and efficient. Similarly, the DNAStringSet (or RNAStringSet, or AAStringSet) class is a container for storing a set of DNAString (or RNAString, or AAString) objects.

The BStringList class (and family) is equivalent to the BStringSet family. It was a first attempt to address the problem of storing a large set of sequences but it has been superseded by the BStringSet family.

Usage

  BStringSet(x, start=NA, end=NA, width=NA, use.names=TRUE)
  DNAStringSet(x, start=NA, end=NA, width=NA, use.names=TRUE)
  RNAStringSet(x, start=NA, end=NA, width=NA, use.names=TRUE)
  AAStringSet(x, start=NA, end=NA, width=NA, use.names=TRUE)

  ## The BStringList family has been superseded by the more efficient
  ## BStringSet family
  BStringList(x, start=NA, end=NA, width=NA, use.names=TRUE, check=TRUE)
  DNAStringList(x, start=NA, end=NA, width=NA, use.names=TRUE, check=TRUE)
  RNAStringList(x, start=NA, end=NA, width=NA, use.names=TRUE, check=TRUE)
  AAStringList(x, start=NA, end=NA, width=NA, use.names=TRUE, check=TRUE)

Arguments

x [TODO]
start [TODO]
end [TODO]
width [TODO]
use.names [TODO]
check [TODO]

Details

[TODO]

Accesor methods

The XStringSet class derives from the IRanges class hence all the accessor methods defined for a IRanges object can also be used on an XStringSet object. In particular, the following methods are available (in the code snippets below, x is an XStringSet object:

length(x): The number of sequences in x.
width(x): A vector of non-negative integers containing the number of letters for each element in x.
nchar(x): The same as width(x).
names(x): NULL or a character vector of the same length as x containing a short user-provided description or comment for each element in x. These are the only data in an XStringSet object that can safely be changed by the user. All the other data are immutable! As a general recommendation, the user should never try to modify an object by accessing its slots directly.

Subsetting methods

In the code snippets below, x is an XStringSet object, and i should be an index specifying the elements to extract.

x[i]: Return a new XStringSet object made of the selected elements.
x[[i]]: Extract the i-th BString object from x.

Other methods

In the code snippets below, x is an XStringSet object.

as.list(x): Return the elements in x as a standard R list.

Author(s)

H. Pages

See Also

BString-class, DNAString-class, RNAString-class, AAString-class, XStringViews-class, IRanges

Examples

  x1 <- DNAStringSet(c("TTGA", "-CTC-N"))
  x1
  names(x1)
  names(x1)[2] <- "seqB"
  x1

  library(drosophila2probe)
  x2 <- DNAStringSet(drosophila2probe$sequence)
  x2

  RNAStringSet(x2, start=2, end=-5)

[Package Biostrings version 2.8.18 Index]