Import/Export Routines for 'MALDIquant'

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.


News

RELEASE HISTORY OF THE "MALDIquantForeign" PACKAGE

CHANGES in MALDIquantForeign VERSION 0.12 [2019-01-30]:

  • Fix reading of mzML with "non-standard data" arrays. Bug reported by Paul Turner.

CHANGES in MALDIquantForeign VERSION 0.11.6 [2018-08-30]:

  • Ignore comments in .autoSep and .autoHeader. Affected functions: .tab and .csv import, import, importCsv, importTab, importTxt. Bug reported by Fernando Pineda.

CHANGES in MALDIquantForeign VERSION 0.11.5 [2018-08-14]:

  • Fix psidev URLs.

CHANGES in MALDIquantForeign VERSION 0.11.4 [2018-08-01]:

BUGFIX

  • Don't access totalIonCurrent for MassPeaks objects in exportMzMl and exportImzMl.

CHANGES in MALDIquantForeign VERSION 0.11.3 [2018-05-27]:

BUGFIX

  • Don't use scientific format for numeric values in (i)mzML export. Patch by F. Orlando Galashan (see #25).

CHANGES in MALDIquantForeign VERSION 0.11.2 [2018-03-18]:

BUGFIX

  • Fix missing unitName in intensity array in mzMl export. Reported by Jan Kobarg patch proposed by F. Orlando Galashan (see #22/#24).

CHANGES IN MALDIquantForeign VERSION 0.11.1 [2017-12-04]:

BUGFIX

  • Fix handling of "processed" argument in .writeImzMlDocument; see #21.
  • Fix export method if there was no filename given.

CHANGES IN MALDIquantForeign VERSION 0.11 [2017-09-01]:

BUGFIX

  • Fix integer overflow in .ibdOffsets; see issue #20.
  • Fix exportImzMl for missing coordinates, pixelSize and dimension; closes
  • #20.

INTERNAL CHANGES

  • Put MALDIquant into single quotes in the DESCRIPTION file.
  • Rezip inst/compressed/csv.tar.gz using gzip -n to avoid lintian's package-contains-timestamped-gzip warning; see https://wiki.debian.org/ReproducibleBuilds for details.

CHANGES IN MALDIquantForeign VERSION 0.10 [2015-10-31]:

IMPROVEMENTS

  • Add parallel support on unix-based platforms using the parallel package. All import* functions support the "mc.cores" argument (default is 1, means no parallel import). Please read also ?"MALDIquantForeign-parallel".
  • Add importer for .msd (mMass) files: importMsd.
  • Add basic export support for imzML files: exportImzMl.
  • .importImzMl: add "coordinates" argument to access specific spectra by their x, y coordinates within an imzML file; closes #14; affected functions: import, importImzMl. Thanks to Heath Patterson [email protected] for this idea.

MODIFICATIONS

  • Remove dependency "downloader". Since R 3.2.2 https is supported on all platforms by base::download.file.
  • Use "verbose = interactive()" in import.
  • Replace old imzML example files in inst/exampledata.
  • exportMzMl: improve documentation of the "path" argument.
  • .importImzMl: if the imzML file doesn't contain any UUID a warning is thrown instead of an error; affected functions: import, importImzMl.
  • .importImzMl: if the imzML file doesn't contain any checksum for its corresponding idb file a warning is thrown (before it was an error); affected functions: import, importImzMl.

INTERNAL CHANGES

  • Import non-base functions/methods via NAMESPACE.
  • Use MALDIquant's new coordinates method.
  • Replace require by requireNamespace as suggested by "Writing R Extensions".
  • Rezip gzip'ed files using gzip -n to avoid lintian's package-contains-timestamped-gzip warning; see https://wiki.debian.org/ReproducibleBuilds for details.

CHANGES IN MALDIquantForeign VERSION 0.9 [2014-08-11]:

IMPROVEMENTS

  • .readAnalyzeIntensity: allow to specify a mass range of interest to reduce memory usage while importing Analyze files; affected functions: import, importAnalyze
  • importAnalyze: use as.double after reading the image dimensions to avoid integer overflows in vector allocations (the Analyze 7.5 format specification limits the dimensions to integer). Thanks to Ken Frankel [email protected] for reporting this problem.
  • importImzMl: add MD5 checksum support for imzML files. Thanks to Ken Frankel [email protected] for reporting this problem.

CHANGES IN MALDIquantForeign VERSION 0.8 [2014-06-16]:

MODIFICATIONS

  • import: set argument centroided=FALSE as default (was NA before). The automatically determination of profile/centroided data was too error prone. Now we read everything as profile data (use centroided=TRUE to read centroided data); affected functions: all import functions (e.g. importBrukerFlex, importMzMl ...).

IMPROVEMENTS

  • importAnalyze: circumvent the limit of 32747 intensity values that is specified in the official Analyze 7.5 format. Thanks to Ken Frankel [email protected] for reporting this problem.

INTERNAL CHANGES

  • Fix VignetteIndexEntry.
  • Rename vignette output file from MALDIquantForeign.pdf to MALDIquantForeign-intro.pdf.
  • Check availability of the "RNetCDF" package in the importCdf man page to avoid build failures on CRAN.
  • Don't evaluate the remote import example in the vignette to avoid build failures on CRAN.

CHANGES IN MALDIquantForeign VERSION 0.7 [2014-04-11]:

IMPROVEMENTS

  • Add vignette.

INTERNAL CHANGES

  • Move tests into tests/testthat to adapt to testthat 0.8 and new CRAN policy; close #10.

  • Fix path of exampledata (needed because the test scripts moved to tests).

CHANGES IN MALDIquantForeign VERSION 0.6 [2014-01-28]:

NEW FEATURES

  • Add basic import support for CDF files [contributed by Pietro Franceschi]; new function: importCdf.
  • import: add arguments "massRange" and "minIntensity" to limit import range; affected functions: all import* functions.
  • import: add argument "centroided" to allow import of centroided spectra as MassPeaks objects; affected functions: all import* functions.

IMPROVEMENTS

  • Add "skip" argument to .importCsv, .importTab, .autoSep and .autoHeader to allow skipping first lines; affected functions: import, importTxt, importTab, importCsv

BUG FIXES

  • importAnalyze: add support for ABSiex Analyze 7.5 files. Thanks to Pietro Franceschi for reporting this bug/odd behaviour.
  • .importTab: use .autoSep and .autoHeader (before they were used only by .importCsv); affected functions: import, importTxt, importTab
  • .parseMzML: fix assignment operation. Before all metaData of spectra were overwritten by the metaData of the last spectrum (affected only mzML files with more than one spectrum). affected functions: importMzML
  • export: fix one file export; additional affected functions: exportMzMl.

INTERNAL CHANGES

  • Regenerate man pages with new 'roxygen2' (3.0.0).

CHANGES IN MALDIquantForeign VERSION 0.5.1 [2013-09-18]:

BUG FIXES

  • Replace MALDIquant:::isMassSpectrum by MALDIquant::isMassSpectrum.
  • Replace deprecated function isMassObjectList.

CHANGES IN MALDIquantForeign VERSION 0.5 [2013-09-08]:

IMPROVEMENTS

  • import*: add "excludePattern" argument to avoid import of specific files; closes #8.

BUGFIXES

  • Fix "totalIonCurrent" test case.
  • Add import("methods") to NAMESPACE (fixes #9).

INTERNAL CHANGES

  • Update dependencies; now MALDIquantForeign depends on R 3.0.0.
  • Replace all paste(..., sep="") by paste0.

CHANGES IN MALDIquantForeign VERSION 0.4 [2013-04-28]:

NEW FEATURES

  • Add basic import support for imzML files and Analyze 7.5 files.

IMPROVEMENTS

  • import: add "removeEmptySpectra" argument; closes #7.

MODIFICATIONS

  • import: change default argument "verbose" to TRUE.

BUGFIXES

  • .download: respects "verbose" argument now (fixes #6).

INTERNAL CHANGES

  • Remove LICENSE file.

CHANGES IN MALDIquantForeign VERSION 0.3 [2013-03-01]:

NEW FEATURES

  • Add basic support for mzML export.
  • Add basic import support for Ciphergen XML files.
  • import: add http(s):// and ftp:// support.
  • import: add uncompression support to allow import of zip/tar.{gz,bz2,xz}-archives.

BUGFIXES

  • Add missing "usage" section in export methods manual pages.
  • .files: returns only unique file names; affected functions: all import functions.

INTERNAL CHANGES

  • .make.unique: generates c("a1", "a2") instead of c("a", "a1") and c("a001", ..., "a099", "a100") instead of c("a", ..., "a98", "a99"); affected method: export,list.
  • DESCRIPTION: move base64enc, digest, readBrukerFlexData, readMzXmlData and XML to "Imports".
  • DESCRIPTION: remove MALDIquant from the "Imports" field.

CHANGES IN MALDIquantForeign VERSION 0.2 [2013-01-14]:

IMPROVEMENTS

  • exportMsd: complete rewrite, write xml files manually instead of using the XML package (increasing speed).

BUGFIXES

  • export: fix empty filenames.
  • export,list: stop if directory doesn't exist.
  • exportMsd: fix peaks argument.
  • exportMsd tests: respect endianness.
  • import: respect verbose argument in import(type="auto").

CHANGES IN MALDIquantForeign VERSION 0.1 [2012-12-10]:

  • First public release.
  • Supported file formats:
    • Import: tab, txt, csv, Bruker Daltonics *flex files, mzXML, mzML
    • Export: tab, csv, msd

Reference manual

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install.packages("MALDIquantForeign")

0.12 by Sebastian Gibb, 3 months ago


http://strimmerlab.org/software/maldiquant/ https://github.com/sgibb/MALDIquantForeign/


Report a bug at https://github.com/sgibb/MALDIquantForeign/issues/


Browse source code at https://github.com/cran/MALDIquantForeign


Authors: Sebastian Gibb [aut, cre] , Pietro Franceschi [ctb]


Documentation:   PDF Manual  


GPL (>= 3) license


Imports base64enc, digest, readBrukerFlexData, readMzXmlData, XML

Depends on methods, MALDIquant

Suggests knitr, testthat, RNetCDF


See at CRAN