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\name{BiocFile-class}
\docType{class}
%% Classes:
\alias{class:BiocFile}
\alias{BiocFile-class}
\alias{class:CompressedFile}
\alias{CompressedFile-class}
\alias{BiocFileList-class}
%% Accessors
\alias{path}
\alias{path,BiocFile-method}
\alias{resource}
\alias{resource<-}
\alias{fileFormat}
\alias{fileFormat,BiocFile-method}
\alias{fileFormat,CompressedFile-method}
\alias{fileFormat,character-method}
%% Consturctors
\alias{BiocFileList}
%% Show:
\alias{show,BiocFile-method}
%% Related functions:
\alias{FileForFormat}
\alias{bestFileFormat}
\alias{bestFileFormat,GRangesList-method}
\alias{bestFileFormat,GenomicRanges-method}
\alias{bestFileFormat,IntegerRangesList-method}
\alias{bestFileFormat,RleList-method}
\alias{decompress}
\alias{decompress,ANY-method}
\alias{decompress,CompressedFile-method}
\alias{decompress,GZFile-method}
\alias{decompress,character-method}
%% Coerce:
\alias{as.character,BiocFile-method}
\title{BiocFile objects}
\description{
A \code{BiocFile} object is the base class for classes representing
files accessible with rtracklayer. It wraps a resource (either a path,
URL or connection). We can represent a list of \code{BiocFile} objects
with a \code{BiocFileList}.
}
\section{Accessor Methods}{
In the code snippets below, \code{x} represents a \code{BiocFile}
object.
\describe{
\item{}{
\code{path(x)}:
Gets the path, as a \code{character} vector, to the resource
represented by the \code{BiocFile} object, if possible.
}
\item{}{
\code{resource(x)}:
Gets the low-level resource, either a character vector (a path or
URL) or a connection.
}
\item{}{
\code{fileFormat(x)}: Gets a string identifying the file
format. Can also be called directly on a character file path, in
which case it uses a heuristic based on the file extension.
}
}
}
\section{Coercion}{
\describe{
\item{}{
\code{as.character(x)}:
Returns the path of the file as a character vector.
}
}
}
\section{Related functions}{
\describe{
\item{}{
\code{FileForFormat(path, format = file_ext(path))}:
Determines the file type of \code{path} and returns
a high-level file object such as BamFile, BEDFile,
BigWigFile etc..
}
\item{}{
\code{bestFileFormat(x)}: Returns the best possible file format for a
given file. This function searches through loaded packages for "File"
classes that contain S4 methods for `export` and `import` for that class.
}
\item{}{
\code{decompress(x)}: Returns a decompressed representation of a
\code{CompressedFile} or \code{character} object.
}
}
}
\examples{
## For our examples, we create a class called CSVFILE that extends BiocFile
.CSVFile <- setClass("CSVFile", contains = "BiocFile")
## Constructor
CSVFile <-
function(resource)
{
.CSVFile(resource = resource)
}
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), ...)
})
## Recommend CSVFile class for .csv files
temp <- tempfile(fileext = ".csv")
FileForFormat(temp)
## Create CSVFile
csv <- CSVFile(temp)
## Display path of file
path(csv)
## Display resource of file
resource(csv)
}
\author{Michael Lawrence}
\seealso{
Implementing classes include: \code{\link[rtracklayer]{BigWigFile}},
\code{\link[rtracklayer]{TwoBitFile}}, \code{\link[rtracklayer]{BEDFile}},
\code{\link[rtracklayer]{GFFFile}}, and \code{\link[rtracklayer]{WIGFile}}.
}
\keyword{methods}
\keyword{classes}
|
