IO: Import and export

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

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

See Also

Format-specific options for the popular formats: GFF, BED, Bed15, bedGraph, WIG, 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)

Bioconductor/BiocIO documentation built on Nov. 1, 2024, 1:46 a.m.