1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
|
\name{as.alignment}
\alias{as.alignment}
\alias{as.DNAbin}
\alias{as.DNAbin.character}
\alias{as.DNAbin.list}
\alias{as.DNAbin.alignment}
\alias{as.character.DNAbin}
\alias{as.DNAbin.DNAString}
\alias{as.DNAbin.DNAStringSet}
\alias{as.DNAbin.PairwiseAlignmentsSingleSubject}
\alias{as.DNAbin.DNAMultipleAlignment}
\title{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, ...)
\method{as.DNAbin}{character}(x, ...)
\method{as.DNAbin}{list}(x, ...)
\method{as.DNAbin}{alignment}(x, ...)
\method{as.DNAbin}{DNAString}(x, ...)
\method{as.DNAbin}{DNAStringSet}(x, ...)
\method{as.DNAbin}{PairwiseAlignmentsSingleSubject}(x, ...)
\method{as.DNAbin}{DNAMultipleAlignment}(x, ...)
\method{as.character}{DNAbin}(x, ...)
}
\arguments{
\item{x}{a matrix or a list containing the DNA sequences, or an object
of class \code{"alignment"}.}
\item{\dots}{further arguments to be passed to or from other methods.}
}
\details{
For \code{as.alignment}, the sequences given as argument should be
stored as matrices or lists of single-character strings (the format
used in \pkg{ape} before version 1.10). The returned object is in the
format used in the package \pkg{seqinr} to store aligned sequences.
\code{as.DNAbin} is a generic function with methods so that it works
with sequences stored into vectors, matrices, or lists. It can convert
some S4 classes from the package \pkg{Biostrings} in BioConductor. For
consistency within \pkg{ape}, this uses an S3-style syntax. To convert
objects of class \code{"DNAStringSetList"}, see the examples.
\code{as.character} is a generic function: the present method
converts objects of class \code{"DNAbin"} into the format used
before \pkg{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 \code{"DNAbin"} into the class \code{"alignment"}.
}
\value{
an object of class \code{"alignment"} in the case of
\code{"as.alignment"}; an object of class \code{"DNAbin"} in the case
of \code{"as.DNAbin"}; a matrix of mode character or a list containing
vectors of mode character in the case of \code{"as.character"}.
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{DNAbin}}, \code{\link{read.dna}},
\code{\link{read.GenBank}}, \code{\link{write.dna}}
}
\examples{
data(woodmouse)
x <- as.character(woodmouse)
x[, 1:20]
str(as.alignment(x))
identical(as.DNAbin(x), woodmouse)
### conversion from BioConductor:
\dontrun{
if (require(Biostrings)) {
data(phiX174Phage)
X <- as.DNAbin(phiX174Phage)
## base frequencies:
base.freq(X) # from ape
alphabetFrequency(phiX174Phage) # from Biostrings
### for objects of class "DNAStringSetList"
X <- lapply(x, as.DNAbin) # a list of lists
### to put all sequences in a single list:
X <- unlist(X, recursive = FALSE)
class(X) <- "DNAbin"
}
}
}
\keyword{manip}
|
