import-functions: Import files

In sgibb/MALDIquantForeign: Import/Export Routines for 'MALDIquant'

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

https://strimmerlab.github.io/software/maldiquant/

See Also

MassSpectrum-class, MassPeaks-class MALDIquantForeign-parallel

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"))

sgibb/MALDIquantForeign documentation built on Jan. 26, 2024, 10:07 a.m.