Version:	0.14.1
Date:	2024-01-22
Title:	Import/Export Routines for 'MALDIquant'
Depends:	R (≥ 3.2.2), methods, MALDIquant (≥ 1.16.4)
Imports:	base64enc, digest, readBrukerFlexData (≥ 1.7), readMzXmlData (≥ 2.7), XML
Suggests:	knitr, testthat (≥ 0.8), RNetCDF (≥ 1.6.1)
Description:	Functions for reading (tab, csv, Bruker fid, Ciphergen XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and writing (tab, csv, mMass MSD, mzML, imzML) different file formats of mass spectrometry data into/from 'MALDIquant' objects.
License:	GPL (≥ 3)
URL:	https://strimmerlab.github.io/software/maldiquant/, https://github.com/sgibb/MALDIquantForeign/
BugReports:	https://github.com/sgibb/MALDIquantForeign/issues/
LazyLoad:	yes
VignetteBuilder:	knitr
RoxygenNote:	7.3.0
Encoding:	UTF-8
NeedsCompilation:	no
Packaged:	2024-01-22 20:59:12 UTC; sebastian
Author:	Sebastian Gibb [aut, cre], Pietro Franceschi [ctb]
Maintainer:	Sebastian Gibb <mail@sebastiangibb.de>
Repository:	CRAN
Date/Publication:	2024-01-22 21:32:54 UTC

Import/Export routines for ‘MALDIquant’

Description

This package reads and writes different file formats of mass spectrometry data into/from ‘MALDIquant’ objects.

Details

Author(s)

Sebastian Gibb mail@sebastiangibb.de

References

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

See Also

Useful links:

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

• https://github.com/sgibb/MALDIquantForeign/

• Report bugs at https://github.com/sgibb/MALDIquantForeign/issues/

Converts double to base64 character.

Description

This function converts a double vector to a base64 encoded character vector.

Usage

.base64encode(
  x,
  size,
  endian = .Platform$endian,
  compressionType = c("none", "gzip")
)

Arguments

Value

Vector of type character.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

base64encode from base64enc package

Parallel Support in Package MALDIquantForeign

Description

MALDIquantForeign-package offers multi-core support using mclapply and mcmapply. This approach is limited to unix-based platforms.

Details

Please note that not all import functions benfit from parallelisation. The current implementation is limited to run the parallelisation over different files. That's why only imports of multiple files could be run on multiple cores. E.g. a single mzML file containing 4 spectra would always be read on a single core. In contrast 4 mzML files each containing just one spectra could be read in using 4 cores.

The improvement in the runtime depends on the amount of data to read, the proportion of parsing/decoding of the data, the amount of memory and the speed of the hard disk.

Please note: It is possible that using parallelisation results in a worse runtime!

Author(s)

Sebastian Gibb mail@sebastiangibb.de

References

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

See Also

MALDIquant-parallel, mclapply, mcmapply

Examples

 ## load packages
 library("MALDIquant")
 library("MALDIquantForeign")

 exampleDirectory <- system.file("exampledata", package="MALDIquantForeign")

 ## run single-core import
 print(system.time(
   s1 <- importMzMl(exampleDirectory, centroided=TRUE, verbose=FALSE)
 ))

 if(.Platform$OS.type == "unix") {
   ## run multi-core import
   ## (because the example spectra are very small (just 5 data points) the
   ## multi-core solution is slower on most systems)
   print(system.time(
     s2 <- importMzMl(exampleDirectory, centroided=TRUE, mc.cores=2,
                      verbose=FALSE)
   ))
   stopifnot(all.equal(s1, s2))
 }

Export files

Description

This function provides a general interface to export AbstractMassObject-class objects (e.g. MassSpectrum-class, MassPeaks-class) into different file formats.

Usage

## S4 method for signature 'AbstractMassObject'
export(x, file, type="auto", force=FALSE, ...)

## S4 method for signature 'list'
export(x, path, type, force=FALSE, ...)

Arguments

Details

Specific export functions:

Author(s)

Sebastian Gibb

References

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

See Also

MassPeaks-class, MassSpectrum-class

Examples

## Not run: 
library("MALDIquant")
library("MALDIquantForeign")

s <- list(createMassSpectrum(mass=1:5, intensity=1:5),
          createMassSpectrum(mass=1:5, intensity=1:5))

## export a single spectrum
export(s[[1]], file="spectrum.csv")
## identical to exportCsv(s[[1]], file="spectrum.csv")

## export a list of spectra
export(s, path="spectra", type="csv")
## identical to exportCsv(s, path="spectra")

## End(Not run)

Export to imzML files

Description

This function exports MassSpectrum-class objects into imzML files.

Usage

## S4 method for signature 'MassSpectrum'
exportImzMl(x, file, force=FALSE, processed=TRUE,
coordinates=NULL, pixelSize=c(100, 100), ...)

## S4 method for signature 'list'
exportImzMl(x, path, force=FALSE, processed=TRUE,
coordinates=NULL, pixelSize=c(100, 100), ...)

Arguments

Author(s)

Sebastian Gibb

References

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

Schramm T, Hester A, Klinkert I, Both J-P, Heeren RMA, Brunelle A, Laprevote O, Desbenoit N, Robbe M-F, Stoeckli M, Spengler B, Roempp A (2012)
imzML - A common data format for the flexible exchange and processing of mass spectrometry imaging data.
Journal of Proteomics 75 (16):5106-5110.
doi:10.1016/j.jprot.2012.07.026

See Also

MassSpectrum-class

Examples

## Not run: 
library("MALDIquant")
library("MALDIquantForeign")

s <- list(createMassSpectrum(mass=1:5, intensity=1:5),
          createMassSpectrum(mass=1:5, intensity=1:5))

## export a list of spectra
exportImzMl(s, path="processed.imzML", coordinates=cbind(x=1:2, y=c(1, 1)))

## End(Not run)

Export to MSD files

Description

This function exports AbstractMassObject-class objects (e.g. MassSpectrum-class, MassPeaks-class) into mMass MSD files.

Usage

## S4 method for signature 'MassSpectrum'
exportMsd(x, file, force=FALSE, peaks, ...)

## S4 method for signature 'list'
exportMsd(x, path, force=FALSE, peaks, ...)

Arguments

Author(s)

Sebastian Gibb

References

https://strimmerlab.github.io/software/maldiquant/,
mMass homepage: http://mmass.org/

See Also

MassPeaks-class, MassSpectrum-class

Examples

## Not run: 
library("MALDIquant")
library("MALDIquantForeign")

s <- list(createMassSpectrum(mass=1:5, intensity=1:5),
          createMassSpectrum(mass=1:5, intensity=1:5))
p <- list(createMassPeaks(mass=4:5, intensity=4:5, snr=1:2),
          createMassPeaks(mass=4:5, intensity=4:5, snr=1:2))

## export a single spectrum
exportMsd(s[[1]], file="spectrum.msd")

## export a single spectrum with corresponding peaks
exportMsd(s[[1]], file="spectrum.msd", peaks=p[[1]])

## export a list of spectra with corresponding peaks
exportMsd(s, path="spectra", peaks=p, force=TRUE)

## End(Not run)

Export to mzML files

Description

This function exports MassSpectrum-class objects into mzML files.

Usage

## S4 method for signature 'MassSpectrum'
exportMzMl(x, file, force=FALSE, ...)

## S4 method for signature 'list'
exportMzMl(x, path, force=FALSE, ...)

Arguments

Author(s)

Sebastian Gibb

References

https://strimmerlab.github.io/software/maldiquant/,
HUPO Proteomics Standards Inititative mzML 1.1.0 Specification: https://www.psidev.info/mzML

See Also

MassSpectrum-class

Examples

## Not run: 
library("MALDIquant")
library("MALDIquantForeign")

s <- list(createMassSpectrum(mass=1:5, intensity=1:5),
          createMassSpectrum(mass=1:5, intensity=1:5))

## export a single spectrum
exportMzMl(s[[1]], file="spectrum.mzML")

## export a list of spectra
exportMzMl(s, path="spectra.mzML")

## End(Not run)

Export to text files

Description

This function exports AbstractMassObject-class objects (e.g. MassSpectrum-class, MassPeaks-class) into different text file formats.

Usage

## S4 method for signature 'AbstractMassObject'
exportTab(x, file, force=FALSE, ...)

## S4 method for signature 'list'
exportTab(x, path, force=FALSE, ...)

## S4 method for signature 'AbstractMassObject'
exportCsv(x, file, force=FALSE, ...)

## S4 method for signature 'list'
exportCsv(x, path, force=FALSE, ...)

Arguments

Details

exportTab and exportCsv use write.table with different defaults (sep="\t" in exportTab and sep="," in exportCsv).

Author(s)

Sebastian Gibb

References

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

See Also

MassPeaks-class, MassSpectrum-class, write.table

Examples

## Not run: 
library("MALDIquant")
library("MALDIquantForeign")

s <- list(createMassSpectrum(mass=1:5, intensity=1:5),
          createMassSpectrum(mass=1:5, intensity=1:5))

## export a single spectrum
exportTab(s[[1]], file="spectrum.tab")

## export a list of spectra and use ; as separator
exportCsv(s, path="spectra", sep=";", force=TRUE)

## End(Not run)

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

Details

Specific import functions:

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"))

Import Analyze 7.5 files

Description

This function imports files in Analyze 7.5 file format into MassSpectrum-class or MassPeaks-class objects.

Usage

importAnalyze(path, ...)

Arguments

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/
http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm, https://eeg.sourceforge.net/ANALYZE75.pdf

See Also

MassSpectrum-class, MassPeaks-class

Import Bruker Daltonics *flex files

Description

This function imports files in Bruker Daltonics *flex-series file format into MassSpectrum-class or MassPeaks-class objects.

Usage

importBrukerFlex(path, ...)

Arguments

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, readBrukerFlexFile

Examples

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

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

s <- importBrukerFlex(exampleDirectory)

Import CDF files

Description

This function imports files in NetCDF file format into MassSpectrum-class or MassPeaks-class objects.
Please note that the RNetCDF is needed.

Usage

importCdf(path, ...)

Arguments

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

Examples

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

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

## import
if (requireNamespace("RNetCDF", quietly=TRUE)) {
  s <- importCdf(exampleDirectory)
} else {
  message("You have to install the RNetCDF package to use importCdf.")
}

Import Ciphergen XML files

Description

This function imports files in Ciphergen XML file format into MassSpectrum-class or MassPeaks-class objects.

Usage

importCiphergenXml(path, ...)

Arguments

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

Examples

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

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

## import
s <- importCiphergenXml(exampleDirectory)

Import imzML files

Description

This function imports files in imzML file format into MassSpectrum-class or MassPeaks-class objects.

Usage

importImzMl(path, coordinates = NULL, ...)

Arguments

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/,
Definition of imzML format: https://ms-imaging.org/imzml/

See Also

MassSpectrum-class, MassPeaks-class

Examples

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

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

## import
s <- importImzMl(file.path(exampleDirectory, "tiny_continuous.imzML"))

## import only spectra for pixel 1,1 and 2,1
s <- importImzMl(file.path(exampleDirectory, "tiny_continuous.imzML"),
                 coordinates = cbind(1:2, c(1, 1)))

Import MSD files

Description

This function imports files in mMass MSD file format into MassSpectrum-class or MassPeaks-class objects.

Usage

importMsd(path, ...)

Arguments

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/,
mMass homepage: http://mmass.org/

See Also

MassSpectrum-class, MassPeaks-class

Examples

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

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

## import
s <- importMsd(exampleDirectory)

Import mzML files

Description

This function imports files in mzML file format into MassSpectrum-class or MassPeaks-class objects.

Usage

importMzMl(path, ...)

Arguments

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/,
Definition of mzML format: https://www.psidev.info/mzML

See Also

MassSpectrum-class, MassPeaks-class

Examples

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

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

## import
s <- importMzMl(exampleDirectory)

Import mzXML files

Description

This function imports files in mzXML file format into MassSpectrum-class or MassPeaks-class objects.

Usage

importMzXml(path, ...)

Arguments

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/,
Definition of mzXML format: http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML

See Also

MassSpectrum-class, MassPeaks-class, readMzXmlFile

Examples

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

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

## import
s <- importMzXml(exampleDirectory)

Import text files

Description

This function imports different text file formats into MassSpectrum-class or MassPeaks-class objects.

Usage

importTxt(path, ...)

importTab(path, ...)

importCsv(path, ...)

Arguments

Details

importTab, importTxt and importCsv use read.table with different defaults.

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, read.table

Examples

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

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

## import txt files
s <- importTxt(exampleDirectory)

## import csv files
s <- importCsv(exampleDirectory)

Supported file formats

Description

This function prints all file formats supported by MALDIquantForeign-package.

Usage

supportedFileFormats()

Details

Import

Export

Value

a list with two named elements (import and export) containing a character vector of supported file types.

Author(s)

Sebastian Gibb

References

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

See Also

export, import

Examples

library("MALDIquantForeign")

supportedFileFormats()