MALDIquantForeign: import-functions – R documentation

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import-functions

Import files

Description

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

Usage

import(path, type = "auto", pattern, excludePattern = NULL,
  removeEmptySpectra = TRUE, centroided = FALSE, massRange = c(0,
  Inf), minIntensity = 0, mc.cores = 1L, verbose = interactive(),
  ...)

Arguments

`path`	`character`, path to directory or file which should be read in.
`type`	`character`, file format. If `type` is set to “auto” MALDIquant tries to detect the correct file type automatically. It often depends on the file extension (if `path` is a directory the most represented file extension is used; `pattern` argument is ignored).
`pattern`	`character`, a regular expression to find files in a directory (see details).
`excludePattern`	`character`, a regular expression to exclude files in a directory (see details).
`removeEmptySpectra`	`logical`, should empty spectra excluded?
`centroided`	`logical`, if `centroided=FALSE` (default) the data are treated as not centroided and a list of `MassSpectrum-class` objects is returned. Use `centroided=TRUE` to assume centroided data and get a list of `MassPeaks-class` objects.
`massRange`	`double`, limits of mass import (left/minimal mass, right/maximal mass).
`minIntensity`	`double`, minimal intensity to import.
`mc.cores`	number of cores to use (default 1; only unix-based platforms are supported, see `MALDIquantForeign-parallel` for details).
`verbose`	`logical`, verbose output?
`...`	arguments to be passed to specific import functions.

Details

Specific import functions:

txt	`importTxt`
tab	`importTab`
csv	`importCsv`
fid	`importBrukerFlex`
ciphergen	`importCiphergenXml`
mzXML	`importMzXml`
mzML	`importMzMl`
imzML	`importImzMl`
analyze	`importAnalyze`
cdf	`importCdf`
msd	`importMsd`

path: In addition to the above mentioned file types the following (compressed) archives are supported, too: zip, tar, tar.gz, tar.bz2, tar.xz. The archives are uncompressed in a temporary directory. Afterwards the import function is called (with type="auto").

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).

excludePattern: Sometimes some files should be excluded. E.g. to ignore additional aquired Bruker LIFT spectra (MALDI-TOF/TOF; which are not support, yet) you could use excludePattern="([[:digit:]\.]+)LIFT[\\/]1SRef".

Value

a list of MassSpectrum-class or MassPeaks-class objects (depending on the centroided argument).

Author(s)

Sebastian Gibb

References

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

Examples

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

## get example directory
exampleDirectory <- system.file("exampledata", 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"))

## import gzipped csv file
s <- import(file.path(exampleDirectory, "compressed", "csv1.csv.gz"))

MALDIquantForeign

Import/Export Routines for 'MALDIquant'

v0.12

GPL (>= 3)

Authors

Sebastian Gibb [aut, cre] (<https://orcid.org/0000-0001-7406-4443>), Pietro Franceschi [ctb]

Initial release

2019-01-30