R: Import and export

IO {BiocIO}

R Documentation

Import and export

Description

The functions import and export load and save objects from and to particular file formats.

Usage

import(con, format, text, ...)

## S4 method for signature 'connection,character,ANY'
import(con, format, text, ...)

## S4 method for signature 'connection,missing,ANY'
import(con, format, text, ...)

## S4 method for signature 'character,missing,ANY'
import(con, format, text, ...)

## S4 method for signature 'character,character,ANY'
import(con, format, text, ...)

## S4 method for signature 'missing,ANY,character'
import(con, format, text, ...)

export(object, con, format, ...)

## S4 method for signature 'ANY,connection,character'
export(object, con, format, ...)

## S4 method for signature 'ANY,connection,missing'
export(object, con, format, ...)

## S4 method for signature 'ANY,missing,character'
export(object, con, format, ...)

## S4 method for signature 'ANY,character,missing'
export(object, con, format, ...)

## S4 method for signature 'ANY,character,character'
export(object, con, format, ...)

## S4 method for signature 'CompressedFile,missing,ANY'
import(con, format, text, ...)

## S4 method for signature 'ANY,CompressedFile,missing'
export(object, con, format, ...)

Arguments

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 file name and a corresponding file connection is created and then closed after exporting the object. If it is a 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.

format

The format of the output. If missing and con is a file name, the format is derived from the file extension. This argument is unnecessary when con is a derivative of BiocFile.

text

If con is missing, this can be a character vector directly providing the string data to import.

...

Parameters to pass to the format-specific method.

object

The object to export.

Value

If con is missing, a character vector containing the string output. Otherwise, nothing is returned.

Author(s)

Michael Lawrence

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)

[Package BiocIO version 1.20.0 Index]