[Seqinr-commits] r1747 - pkg/man

[noreply at r-forge.r-project.org]

Author: lobry
Date: 2010-05-24 11:28:25 +0200 (Mon, 24 May 2010)
New Revision: 1747

Added:
   pkg/man/as.alignment.Rd
Log:
 

Added: pkg/man/as.alignment.Rd
===================================================================
--- pkg/man/as.alignment.Rd	                        (rev 0)
+++ pkg/man/as.alignment.Rd	2010-05-24 09:28:25 UTC (rev 1747)
@@ -0,0 +1,38 @@
+\name{as.alignment}
+\alias{as.alignment}
+\title{Constructor for class alignment}
+\description{
+Returns an object of (S3) class alignment. 
+}
+\usage{
+as.alignment(nb = NULL, nam = NULL, seq = NULL, com = NULL)
+}
+\arguments{
+  \item{nb}{integer. The number of sequences in the alignment.}
+  \item{nam}{vector of \code{nb} character strings. The sequence names. }
+  \item{seq}{vector of \code{nb} character strings. The aligned sequences.}
+  \item{com}{vector of \code{nb} character strings. The comments about sequences.}
+}
+
+\value{
+ An object of class \code{alignment} which is a list with the following components:
+  \item{nb}{ the number of aligned sequences }
+  \item{nam}{ a vector of strings containing the names of the aligned sequences } 
+  \item{seq}{ a vector of strings containing the aligned sequences} 
+  \item{com}{ a vector of strings containing the commentaries for each sequence or \code{NA} if there are no comments }
+}
+\references{ 
+\code{citation("seqinr")}
+}
+\author{ D. Charif, J.R. Lobry }
+\seealso{
+\code{\link{read.alignment}},
+\code{\link{as.matrix.alignment}}, \code{\link{read.fasta}}, 
+\code{\link{write.fasta}}, \code{\link{reverse.align}}, \code{\link{dist.alignment}}.
+
+ }
+\examples{
+as.alignment(nb = 2, nam = c("one", "two"), 
+  seq = c("-ACGT", "GACG-"), com = c("un", "deux"))
+}
+