MALDIquantForeign (version 0.2)

import: Import files

Description

This function provides a general interface to import different file formats into MassSpectrum-class objects.

Usage

import(path, type = "auto", pattern, verbose = FALSE,
    ...)

Arguments

path

character, path to directory or file which should be read in.

type

character, file format. If type is set to auto the file extension (if path is a directory the most represented file extension) is used.

pattern

character, a regular expression to find files in a directory (see details).

verbose

logical, verbose output?

...

arguments to be passed to specific import functions.

Value

• a list of MassSpectrum-class objects.

Details

Specific import functions: ll{ txt importTxt tab importTab csv importCsv fid importBrukerFlex mzXML importMzXml mzML importMzMl }

pattern: Sometimes unusual file extensions are used (e.g. "*.xml" for mzXML files). In this case a specific pattern could be defined to import files with an unusual file extension (e.g. pattern="^.*\.xml$" to read all *.xml files in a directory; see regexp for details).

References

http://strimmerlab.org/software/maldiquant/

See Also

MassSpectrum-class

Examples

library("MALDIquant")
library("MALDIquantForeign")

## get example directory
exampleDirectory <- system.file(file.path("tests", "data"),
                                package="MALDIquantForeign")

## import mzXML files
s <- import(exampleDirectory, type="mzXML")

## import tab delimited file with different file extension (default: *.tab)
s <- import(exampleDirectory, type="tab", pattern="^.*\\.txt")

## import single mzML file
s <- import(file.path(exampleDirectory, "tiny1.mzML1.1.mzML"))