[adegenet-commits] r1043 - pkg/man

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

Author: jombart
Date: 2012-10-31 16:55:45 +0100 (Wed, 31 Oct 2012)
New Revision: 1043

Added:
   pkg/man/fasta2DNAbin.Rd
Log:
forgot to add doc for fasta2DNAbin

Added: pkg/man/fasta2DNAbin.Rd
===================================================================
--- pkg/man/fasta2DNAbin.Rd	                        (rev 0)
+++ pkg/man/fasta2DNAbin.Rd	2012-10-31 15:55:45 UTC (rev 1043)
@@ -0,0 +1,60 @@
+\encoding{UTF-8}
+\name{fasta2DNAbin}
+\alias{fasta2DNAbin}
+\title{ Read large DNA alignments into R}
+\description{
+  The function \code{fasta2DNAbin} reads alignments with the fasta
+  format (extensions ".fasta", ".fas", or ".fa"), and outputs a
+  \code{\link[ape]{DNAbin}} object (the efficient DNA representation from the
+  ape package). The output contains either the full alignments, or only
+  SNPs. This implementation is designed for memory-efficiency,
+  and can read in larger datasets than Ape's \code{\link[ape]{read.dna}}.
+
+  The function reads data by chunks of a few genomes (minimum 1, no
+  maximum) at a time, which allows one to read massive datasets with
+  negligible RAM requirements (albeit at a cost of computational
+  time). The argument \code{chunkSize} indicates the number of genomes
+  read at a time. Increasing this value decreases the computational time
+  required to read data in, while increasing memory requirements.
+
+}
+\usage{
+fasta2DNAbin(file, quiet=FALSE, chunkSize=10, snpOnly=FALSE)
+}
+\arguments{
+  \item{file}{ a character string giving the path to the file to
+    convert, with the extension ".fa", ".fas", or ".fasta".}
+  \item{quiet}{a logical stating whether a conversion messages should be
+    printed (FALSE, default) or not (TRUE).}
+  \item{chunkSize}{an integer indicating the number of genomes to be
+    read at a time; larger values require more RAM but decrease the time
+    needed to read the data.}
+  \item{snpOnly}{a logical indicating whether SNPs only should be returned.}
+}
+\value{an object of the class \code{\link[ape]{DNAbin}}}
+\seealso{
+  - \code{?DNAbin} for a description of the class \code{\link[ape]{DNAbin}}.
+
+  - \code{\link{read.snp}}: read SNPs in adegenet's '.snp' format.
+
+  - \code{\link{read.PLINK}}: read SNPs in PLINK's '.raw' format.
+
+  - \code{\link{df2genind}}: convert any multiallelic markers into
+  adegenet \linkS4class{genind}.
+
+  - \code{\link{import2genind}}: read multiallelic markers from various
+  software into adegenet.
+}
+\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk} }
+\examples{
+## show the example file ##
+## this is the path to the file:
+myPath <- system.file("files/usflu.fasta",package="adegenet")
+myPath
+
+## read the file
+obj <- fasta2DNAbin(myPath, chunk=10) # process 10 sequences at a time
+obj
+
+}
+\keyword{manip}