[Seqinr-commits] r1502 - pkg/man

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

Author: lobry
Date: 2008-11-03 11:37:58 +0100 (Mon, 03 Nov 2008)
New Revision: 1502

Added:
   pkg/man/read.abif.Rd
Log:
new function read.abif

Added: pkg/man/read.abif.Rd
===================================================================
--- pkg/man/read.abif.Rd	                        (rev 0)
+++ pkg/man/read.abif.Rd	2008-11-03 10:37:58 UTC (rev 1502)
@@ -0,0 +1,41 @@
+\name{read.abif}
+\alias{read.abif}
+\title{Read ABIF formatted files}
+\description{
+ABIF stands for Applied Biosystem Inc. Format, a binary fromat modeled after TIFF format.
+Corresponding files usually have an \code{*.ab1} or \code{*.fsa} extension.
+}
+\usage{
+read.abif(filename, max.bytes.in.file = file.info(filename)$size, pied.de.pilote = 1.2, verbose = FALSE)
+}
+\arguments{
+  \item{filename}{The name of the file.}
+  \item{max.bytes.in.file}{The size in bytes of the file, defaulting to what is returned by \code{\link{file.info}}}	
+  \item{pied.de.pilote}{Safety factor: the argument \code{n} to \code{\link{readBin}} is set as \code{pied.de.pilote*max.bytes.in.file}.}	
+  \item{verbose}{logical [FALSE]. If TRUE verbose mode is on.}	
+}
+\details{
+This function is experiemental and has not been intensively tested. All data are imported
+into memory, there is no attempt to read items on the fly.
+}
+\value{
+A list with three components: \code{Header} which is a list that contains various low-level information,
+among which \code{numelements} is the number of elements in the directory and \code{dataoffset}
+the offset to find the location of the directory. \code{Directory} is a data.frame for the directory
+of the file with the number of row being the number of elements in the directory and the 7
+columns describing various low-level information about the elements. \code{Data} is a list
+with the number of components equal to the number of elements in the directory. 
+}
+\references{ 
+\code{citation("seqinR")}
+
+Anonymous (2006) Applied Biosystem Genetic Analysis Data File Format.
+Available at \url{http://www.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf}.
+Last visited on 03-NOV-2008.
+}
+\author{J.R. Lobry}
+\seealso{\code{\link{readBin}} which is used here to import the binary file and \code{\link{file.info}} to
+get the size of the file.}
+\examples{
+# An example is needed here (read a file and check with data(something)
+}