as.alignment: Conversion Among DNA Sequence Internal Formats
Description
These functions transform a set of DNA sequences among various
internal formats.
Usage
as.alignment(x)
as.DNAbin(x, ...)
## S3 method for class 'character':
as.DNAbin(x, ...)
## S3 method for class 'list':
as.DNAbin(x, ...)
## S3 method for class 'alignment':
as.DNAbin(x, ...)
## S3 method for class 'DNAbin':
as.character(x, ...)
Arguments
x
a matrix or a list containing the DNA sequences, or an object
of class "alignment".
...
further arguments to be passed to or from other methods.
Value
an object of class "alignment" in the case of
"as.alignment"; an object of class "DNAbin" in the case
of "as.DNAbin"; a matrix of mode character or a list containing
vectors of mode character in the case of "as.character".
Details
For as.alignment, the sequences given as argument should be
stored as matrices or lists of single-character strings (the format
used in ape before version 1.10). The returned object is in the
format used in the package seqinr to store aligned sequences.
as.DNAbin is a generic function with methods so that it works
with sequences stored into vectors, matrices, or lists.
as.character is a generic function: the present method
converts objects of class "DNAbin" into the format used
before ape 1.10 (matrix of single characters, or list of vectors
of single characters). This function must be used first to convert
objects of class "DNAbin" into the class "alignment".