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\name{write.cross}
\alias{write.cross}
\title{Write data for a QTL experiment to a file}
\description{
Data for a QTL experiment is written to a file (or files).
}
\usage{
write.cross(cross, format=c("csv", "csvr", "csvs", "csvsr",
"mm", "qtlcart", "gary"),
filestem="data", chr, digits=5)
}
\arguments{
\item{cross}{An object of class \code{cross}. See
\code{\link[qtl]{read.cross}} for details.}
\item{format}{Specifies whether to write the data in comma-delimited,
rotated comma-delimited, Mapmaker, QTL Cartographer, or Gary
Churchill's format.}
\item{filestem}{A character string giving the first part of the output
file names (the bit before the dot). In Windows, use forward
slashes (\code{"/"}) or double backslashes (\code{"\\\\"}) to
specify directory trees.}
\item{chr}{A vector specifying for which chromosomes genotype data
should be written.}
\item{digits}{Number of digits to which phenotype values should be
rounded.}
}
%\value{
% Data is written to a single file (comma-delimited format) or two files
% (Mapmaker format).
%}
\details{
Comma-delimited formats: a single csv file is created in the formats
\code{"csv"} or \code{"csvr"}. Two files are created (one for the
genotype data and one for the phenotype data) for the formats
\code{"csvs"} and \code{"csvsr"}; if \code{filestem="file"}, the two
files will be names \code{"file_gen.csv"} and \code{"file_phe.csv"}.
See the help file for \code{\link[qtl]{read.cross}} for details on these formats.
Mapmaker format: Data is written to two files.
Suppose \code{filestem="file"}. Then \code{"file.raw"} will contain
the genotype and phenotype data, and \code{"file.prep"} will contain
the necessary code for defining the chromosome assignments, marker
order, and inter-marker distances.
QTL Cartographer format: Data is written to two files. Suppose
\code{filestem="file"}. Then \code{"file.cro"} will contain
the genotype and phenotype data, and \code{"file.map"} will contain
the genetic map information. Note that cross types are converted to
QTL Cartographer cross types as follows: riself to RF1, risib to RF2,
bc to B1 and f2 to RF2.
Gary's format: Data is written to six files. They are: \cr
\code{"geno.data"} - genotype data; \cr
\code{"pheno.data"} - phenotype data; \cr
\code{"chrid.dat"} - the chromosome identifier for each marker; \cr
\code{"mnames.txt"} - the marker names; \cr
\code{"markerpos.txt"} - the marker positions; \cr
\code{"pnames.txt"} - the phenotype names
}
\examples{
\dontrun{data(fake.bc)
# comma-delimited format
write.cross(fake.bc, "csv", "Data/fakebc", c(1,5,13))
# rotated comma-delimited format
write.cross(fake.bc, "csvr", "Data/fakebc", c(1,5,13))
# split comma-delimited format
write.cross(fake.bc, "csvs", "Data/fakebc", c(1,5,13))
# split and rotated comma-delimited format
write.cross(fake.bc, "csvsr", "Data/fakebc", c(1,5,13))
# Mapmaker format
write.cross(fake.bc, "mm", "Data/fakebc", c(1,5,13))
# QTL Cartographer format
write.cross(fake.bc, "qtlcart", "Data/fakebc", c(1,5,13))
# Gary's format
write.cross(fake.bc, "gary", c(1,5,13))} }
\author{Karl W Broman, \email{kbroman@biostat.wisc.edu}; Hao Wu; Brian S. Yandell}
\seealso{ \code{\link[qtl]{read.cross}} }
\keyword{IO}
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