\name{DNAbin}
\alias{DNAbin}
\alias{print.DNAbin}
-\alias{summary.DNAbin}
\alias{[.DNAbin}
\alias{rbind.DNAbin}
\alias{cbind.DNAbin}
\alias{as.matrix.DNAbin}
+\alias{c.DNAbin}
+\alias{as.list.DNAbin}
+\alias{labels.DNAbin}
\title{Manipulate DNA Sequences in Bit-Level Format}
\description{
These functions help to manipulate DNA sequences coded in the
bit-level coding scheme.
}
\usage{
-\method{print}{DNAbin}(x, \dots)
-\method{summary}{DNAbin}(object, printlen = 6, digits = 3, \dots)
+\method{print}{DNAbin}(x, printlen = 6, digits = 3, \dots)
\method{rbind}{DNAbin}(\dots)
-\method{cbind}{DNAbin}(\dots, check.names = TRUE)
-\method{[}{DNAbin}(x, i, j, drop = TRUE)
+\method{cbind}{DNAbin}(\dots, check.names = TRUE, fill.with.gaps = FALSE,
+ quiet = FALSE)
+\method{[}{DNAbin}(x, i, j, drop = FALSE)
\method{as.matrix}{DNAbin}(x, \dots)
+\method{c}{DNAbin}(\dots, recursive = FALSE)
+\method{as.list}{DNAbin}(x, \dots)
+\method{labels}{DNAbin}(object, \dots)
}
\arguments{
\item{x, object}{an object of class \code{"DNAbin"}.}
\item{\dots}{either further arguments to be passed to or from other
- methods in the case of \code{print}, \code{summary}, and
- \code{as.matrix}, or a series of objects of class \code{"DNAbin"} in
- the case of \code{rbind} and \code{cbind}.}
+ methods in the case of \code{print}, \code{as.matrix}, and
+ \code{labels}, or a series of objects of class \code{"DNAbin"} in the
+ case of \code{rbind}, \code{cbind}, and \code{c}.}
\item{printlen}{the number of labels to print (6 by default).}
\item{digits}{the number of digits to print (3 by default).}
\item{check.names}{a logical specifying whether to check the rownames
before binding the columns (see details).}
+ \item{fill.with.gaps}{a logical indicating whether to keep all
+ possible individuals as indicating by the rownames, and eventually
+ filling the missing data with insertion gaps (ignored if
+ \code{check.names = FALSE}).}
+ \item{quiet}{a logical to switch off warning messages when some rows
+ are dropped.}
\item{i, j}{indices of the rows and/or columns to select or to drop.
They may be numeric, logical, or character (in the same way than for
standard R objects).}
- \item{drop}{logical; if \code{TRUE} (the default), the returned object
- is of the lowest possible dimension.}
+ \item{drop}{logical; if \code{TRUE}, the returned object is of the
+ lowest possible dimension.}
+ \item{recursive}{for compatibility with the generic (unused).}
}
\details{
These are all `methods' of generic functions which are here applied to
DNA sequences stored as objects of class \code{"DNAbin"}. They are
used in the same way than the standard R functions to manipulate
vectors, matrices, and lists. Additionally, the operators \code{[[}
- and \code{$} may be used to extract a vector from a list.
+ and \code{$} may be used to extract a vector from a list. Note that
+ the default of \code{drop} is not the same than the generic operator:
+ this is to avoid dropping rownames when selecting a single sequence.
These functions are provided to manipulate easily DNA sequences coded
with the bit-level coding scheme. The latter allows much faster
comparisons of sequences, as well as storing them in less memory
compared to the format used before \pkg{ape} 1.10.
- For \code{cbind}, if \code{"check.names = TRUE"}, the rownames of each
- matrix are checked, and the rows are reordered if necessary. If the
- rownames differ among matrices, an error occurs. If
- \code{"check.names = FALSE"}, the matrices are simply binded and the
- rownames of the first matrix are used.
+ For \code{cbind}, the default behaviour is to keep only individuals
+ (as indicated by the rownames) for which there are no missing data. If
+ \code{fill.with.gaps = TRUE}, a `complete' matrix is returned,
+ enventually with insertion gaps as missing data. If \code{check.names
+ = TRUE} (the default), the rownames of each matrix are checked, and
+ the rows are reordered if necessary. If \code{check.names = FALSE},
+ the matrices must all have the same number of rows, and are simply
+ binded; the rownames of the first matrix are used. See the examples.
\code{as.matrix} may be used to convert DNA sequences (of the same
length) stored in a list into a matrix while keeping the names and the
- class.
+ class. \code{as.list} does the reverse operation.
}
\value{
an object of class \code{"DNAbin"} in the case of \code{rbind},
Paradis, E. (2007) A Bit-Level Coding Scheme for Nucleotides.
\url{http://ape.mpl.ird.fr/misc/BitLevelCodingScheme_20April2007.pdf}
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\seealso{
\code{\link{as.DNAbin}}, \code{\link{read.dna}},
- \code{\link{read.GenBank}}, \code{\link{write.dna}}
+ \code{\link{read.GenBank}}, \code{\link{write.dna}}, ,
+ \code{\link{image.DNAbin}}
The corresponding generic functions are documented in the package
\pkg{base}.
\examples{
data(woodmouse)
woodmouse
-summary(woodmouse)
-summary(woodmouse, 15, 6)
-summary(woodmouse[1:5, 1:300], 15, 6)
+print(woodmouse, 15, 6)
+print(woodmouse[1:5, 1:300], 15, 6)
### Just to show how distances could be influenced by sampling:
dist.dna(woodmouse[1:2, ])
dist.dna(woodmouse[1:3, ])
+### cbind and its options:
+x <- woodmouse[1:2, 1:5]
+y <- woodmouse[2:4, 6:10]
+as.character(cbind(x, y)) # gives warning
+as.character(cbind(x, y, fill.with.gaps = TRUE))
+\dontrun{
+as.character(cbind(x, y, check.names = FALSE)) # gives an error
+}
}
\keyword{manip}