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\name{io}
\alias{export}
\alias{export,ANY,connection,character-method}
\alias{export,ANY,connection,missing-method}
\alias{export,ANY,CompressedFile,missing-method}
\alias{export,ANY,missing,character-method}
\alias{export,ANY,character,missing-method}
\alias{export,ANY,character,character-method}
\alias{import}
\alias{import,connection,character,ANY-method}
\alias{import,connection,missing,ANY-method}
\alias{import,CompressedFile,missing,ANY-method}
\alias{import,character,missing,ANY-method}
\alias{import,character,character,ANY-method}
\alias{import,missing,ANY,character-method}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Import and export }
\description{
The functions \code{import} and \code{export} load and save
objects from and to particular file formats. The rtracklayer package
implements support for a number of annotation and sequence formats.
}
\usage{
export(object, con, format, ...)
import(con, format, text, ...)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
\item{object}{ The object to export. }
\item{con}{ The connection from which data is loaded or to which data
is saved. If this is a character vector, it is assumed to be a
filename and a corresponding file connection is created and then
closed after exporting the object. If a \code{\linkS4class{BiocFile}}
derivative, the data is loaded from or saved to the underlying
resource. If missing, the function will return the output as a
character vector, rather than writing to a connection.
}
\item{format}{ The format of the output. If missing and \code{con} is
a filename, the format is derived from the file extension. This
argument is unnecessary when \code{con} is a derivative of
\code{\linkS4class{BiocFile}}.
}
\item{text}{ If \code{con} is missing, this can be a character vector
directly providing the string data to import. }
\item{\dots}{ Parameters to pass to the format-specific method.
}
}
\value{
If \code{con} is missing, a character vector containing the string
output. Otherwise, nothing is returned.
}
\author{ Michael Lawrence }
\seealso{
Format-specific options for the popular formats:
\acronym{\link[rtracklayer:GFFFile]{GFF}},
\acronym{\link[rtracklayer:BEDFile]{BED}},
\acronym{\link[rtracklayer:BED15File]{Bed15}},
\acronym{\link[rtracklayer:BEDGraphFile]{bedGraph}},
\acronym{\link[rtracklayer:WIGFile]{WIG}},
\acronym{\link[rtracklayer:BigWigFile]{BigWig}}
}
\examples{
## To illustrate export(), import(), and yeild(), we create a class, CSVFILE
.CSVFile <- setClass("CSVFile", contains = "BiocFile")
## Constructor
CSVFile <-
function(resource)
{
.CSVFile(resource = resource)
}
## Define import
setMethod("import", "CSVFile",
function(con, format, text, ...)
{
read.csv(resource(con), ...)
})
## Define export
setMethod("export", c("data.frame", "CSVFile"),
function(object, con, format, ...)
{
write.csv(object, resource(con), ...)
})
## Usage
temp <- tempfile(fileext = ".csv")
csv <- CSVFile(temp)
export(mtcars, csv)
df <- import(csv)
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\keyword{IO}
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