BiocFile-class: BiocFile class objects

In Bioconductor/BiocIO: Standard Input and Output for Bioconductor Packages

BiocFile class objects

Description

BiocFile is the base virtual class for high-level file abstractions where subclasses are associated with a particular file format or type. It wraps a low-level representation of a file, currently either a path, URL, or connection object. We can represent a list of BiocFile objects with a BiocFileList.

Usage

BiocFileList(files)

resource(x)

resource(x) <- value

## S4 method for signature 'BiocFile'
resource(x)

## S4 replacement method for signature 'BiocFile,character_OR_connection'
resource(x) <- value

fileFormat(x)

## S4 method for signature 'character'
fileFormat(x)

## S4 method for signature 'BiocFile'
fileFormat(x)

## S4 method for signature 'BiocFile'
path(object, ...)

## S4 method for signature 'BiocFile'
show(object)

FileForFormat(path, format = file_ext(path))

## S4 method for signature 'BiocFile'
as.character(x)

Arguments

files	character() A vector of file paths for the BiocFileList constructor
x	A BiocFile instance
object	A BiocFile instance
...	additional arguments to lower-level functions, not used.
path, value	Either a character or connection object to replace the original resource
format	character(1) The file extension conducive to a file class name, e.g., CSVFile

Value

For constructors, an instance of that class. For extractors such as resource and path, typically a character vector of the file path. For FileForFormat, a convenient instance of the class for which the input file corresponds to.

Accessor Methods

In the code snippets below, x represents a BiocFile object.

path(x)

Gets the path, as a character vector, to the resource represented by the BiocFile object, if possible.

resource(x)

Gets the low-level resource, either a character vector (a path or URL) or a connection.

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.

Author(s)

Michael Lawrence

See Also

Implementing classes include: BigWigFile, TwoBitFile, BEDFile, GFFFile, WIGFile

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)

Bioconductor/BiocIO documentation built on April 29, 2023, 8:01 p.m.