new code for reading FASTA files

[ape.git] / man / DNAbin.Rd

diff --git a/man/DNAbin.Rd b/man/DNAbin.Rd
index 87ec965461b4ff0dfcfeaea23027218d2512a9ce..020f6f7fd1de26173aa897a8fa1adf8dd80d8945 100644 (file)
--- a/man/DNAbin.Rd
+++ b/man/DNAbin.Rd
@@ -1,31 +1,35 @@
 \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, fill.with.gaps = FALSE,
              quiet = FALSE)
-\method{[}{DNAbin}(x, i, j, drop = TRUE)
+\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
@@ -38,16 +42,19 @@
     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.}
+    standard \R objects).}
+  \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
+  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
@@ -65,7 +72,7 @@
 
   \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},
@@ -74,11 +81,15 @@
 \references{
   Paradis, E. (2007) A Bit-Level Coding Scheme for Nucleotides.
   \url{http://ape.mpl.ird.fr/misc/BitLevelCodingScheme_20April2007.pdf}
+
+  Paradis, E. (2012) \emph{Analysis of Phylogenetics and Evolution with
+  R (Second Edition).} New York: Springer.
 }
-\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}.
@@ -86,9 +97,8 @@
 \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, ])