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\name{readExpressionSet}
\alias{readExpressionSet}
\concept{ExpressionSet}
\title{Read 'ExpressionSet'}
\description{
Create an instance of class ExpressionSet by reading data from files.
\sQuote{widget} functionality is not implemented for readExpressionSet.
}
\usage{
readExpressionSet(exprsFile,
phenoDataFile,
experimentDataFile,
notesFile,
path,
annotation,
## arguments to read.* methods
exprsArgs=list(sep=sep, header=header, row.names=row.names,
quote=quote, ...),
phenoDataArgs=list(sep=sep, header=header, row.names=row.names,
quote=quote, stringsAsFactors=stringsAsFactors, ...),
experimentDataArgs=list(sep=sep, header=header,
row.names=row.names, quote=quote,
stringsAsFactors=stringsAsFactors, ...),
sep = "\t", header = TRUE, quote = "", stringsAsFactors = FALSE,
row.names = 1L,
## widget
widget = getOption("BioC")$Base$use.widgets,
...)
}
\arguments{
\item{exprsFile}{(character) File or connection from which to read expression
values. The file should contain a matrix with rows as features and
columns as samples. \code{\link{read.table}} is called with this
as its \code{file} argument and further arguments given by \code{exprsArgs}.}
\item{phenoDataFile}{(character) File or connection from which to read
phenotypic data. \code{\link{read.AnnotatedDataFrame}} is called
with this as its \code{file} argument and further arguments given by
\code{phenoDataArgs}.}
\item{experimentDataFile}{(character) File or connection from which to read
experiment data. \code{\link{read.MIAME}} is called with this
as its \code{file} argument and further arguments given by
\code{experimentDataArgs}.}
\item{notesFile}{(character) File or connection from which to read notes;
\code{\link{readLines}} is used to input the file.}
\item{path}{(optional) directory in which to find all the above files.}
\item{annotation}{(character) A single character string indicating the
annotation associated with this ExpressionSet.}
\item{exprsArgs}{A list of arguments to be used with
\code{\link{read.table}} when reading in the expression matrix.}
\item{phenoDataArgs}{A list of arguments to be used (with
\code{\link{read.AnnotatedDataFrame}}) when reading
the phenotypic data.}
\item{experimentDataArgs}{A list of arguments to be used (with
\code{\link{read.MIAME}}) when reading the experiment data.}
\item{sep, header, quote, stringsAsFactors, row.names}{arguments used
by the \code{\link{read.table}}-like functions.}
\item{widget}{A boolean value indicating whether widgets can be
used. Widgets are NOT yet implemented for
\code{read.AnnotatedDataFrame}.}
\item{\dots}{Further arguments that can be passed on to the
\code{\link{read.table}}-like functions.}
}
\details{
Expression values are read using the \code{\link{read.table}}
function. Phenotypic data are read using the
\code{\link{read.AnnotatedDataFrame}} function. Experiment data are
read using the \code{\link{read.MIAME}} function. Notes are read using
the \code{\link{readLines}} function. The return value must be a valid
\code{ExpressionSet}. Only the \code{exprsFile} argument is required.
}
\value{
An instance of the \code{\linkS4class{ExpressionSet}} class.
}
\author{Martin Morgan <mtmorgan@fhcrc.org>}
\seealso{\code{\link{ExpressionSet}} for additional methods.}
\examples{
exprsFile = system.file("extdata", "exprsData.txt", package="Biobase")
phenoFile = system.file("extdata", "pData.txt", package="Biobase")
## Read ExpressionSet with appropriate parameters
obj = readExpressionSet(exprsFile, phenoFile, sep = "\t", header=TRUE)
obj
}
\keyword{file}
\keyword{manip}
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