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\name{read.AnnotatedDataFrame}
\alias{read.AnnotatedDataFrame}
\alias{write.AnnotatedDataFrame}
\concept{AnnotatedDataFrame}
\title{Read and write 'AnnotatedDataFrame'}
\description{
Create an instance of class AnnotatedDataFrame by reading a file, or
save an AnnotatedDataFrame to a file.
}
\usage{
read.AnnotatedDataFrame(filename, path,
sep = "\t", header = TRUE, quote = "", stringsAsFactors = FALSE,
row.names = 1L,
varMetadata.char="#",
widget = getOption("BioC")$Base$use.widgets,
sampleNames = character(0), ...)
write.AnnotatedDataFrame(x, file="", varMetadata.char="#", ...,
append=FALSE, fileEncoding="")
}
\arguments{
\item{filename, file}{file or connection from which to read / write.}
\item{x}{An instance of class \code{AnnotatedDataFrame}.}
\item{path}{(optional) directory in which to find \code{filename}.}
\item{row.names}{this argument gets passed on to
\code{\link{read.table}} and will be used for the row names of the
phenoData slot.}
\item{varMetadata.char}{lines beginning with this character are used
for the \code{varMetadata} slot. See examples.}
\item{sep, header, quote, stringsAsFactors, ...}{further arguments
that get passed on to \code{\link{read.table}} or \code{write.table}.}
\item{widget}{logical. Currently this is \emph{not} implemented, and
setting this option to \code{TRUE} will result in an error. In a
precursor of this function, \code{read.phenoData}, this option could
be used to open an interactive GUI widget for entering the data.}
\item{sampleNames}{optional argument that could be used in conjunction
with \code{widget}; do not use.}
\item{append, fileEncoding}{Arguments as described in
\code{\link{write.table}}}.
}
\details{
The function \code{\link{read.table}} is used to read
\code{pData}. The argument \code{varMetadata.char} is passed on to
that function as its argument \code{comment.char}.
Lines beginning with \code{varMetadata.char} are expected to contain
further information on the column headers of \code{pData}.
The format is of the form: \code{# variable: textual explanation of the
variable, units, measurement method, etc.} (assuming that \code{#}
is the value of \code{varMetadata.char}). See also examples.
\code{write.AnnotatedDataFrame} outputs \code{varLabels} and
\code{varMetadata(x)$labelDescription} as commented header lines, and
\code{pData(x)} as a with \code{write.table}.
}
\value{
\code{read.AnnotatedDataFrame}: An instance of class
\code{AnnotatedDataFrame}
\code{write.AnnotatedDataFrame}: \code{NULL}, invisibly.
}
\author{Martin Morgan <mtmorgan@fhcrc.org> and Wolfgang Huber,
based on \code{read.phenoData} by Rafael A. Irizarry.}
\seealso{\code{\link{AnnotatedDataFrame}} for additional methods,
\code{\link{read.table}} for details of reading in phenotypic data}
\examples{
exampleFile = system.file("extdata", "pData.txt", package="Biobase")
adf <- read.AnnotatedDataFrame(exampleFile)
adf
head(pData(adf))
head(noquote(readLines(exampleFile)), 11)
write.AnnotatedDataFrame(adf) # write to console by default
}
\keyword{file}
\keyword{manip}
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