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Workflow solutions for mass-spectrometry based non-target analysis.

Source: R/main.R
patRoon-package.Rd

Provides an easy-to-use interface to a mass spectrometry based non-target analysis workflow. Various (open-source) tools are combined which provide algorithms for extraction and grouping of features, extraction of MS and MS/MS data, automatic formula and compound annotation and grouping related features to components. In addition, various tools are provided for e.g. data preparation and cleanup, plotting results and automatic reporting.

Package options

The following package options (see options) can be set:

  • patRoon.cache.mode: A character setting the current caching mode: "save" and "load" will only save/load results to/from the cache, "both" (default) will do both and "none" to completely disable caching. This option can be changed anytime, which might be useful, for instance, to temporarily disable cached results before running a function.

  • patRoon.cache.fileName: a character specifying the name of the cache file (default is cache.sqlite).

  • patRoon.cache.maxEntries: a numeric specifying the maximum number of entries per cache category (default is 100000). When this limit is exceeded, the oldest entries are automatically removed.

  • patRoon.MS.backends,patRoon.MS.preferIMS,patRoon.path.TDFSDK: Options related to the raw data interface.

  • patRoon.threads: The number of threads to be used for parallelization. This is currently only used by the raw data interface and when the piek algorithm is used for peak detection.

  • patRoon.MP.maxProcs: The maximum number of processes that should be initiated in parallel. A good starting point is the number of physical cores, which is the default as detected by detectCores. This option is only used when patRoon.MP.method="classic".

  • patRoon.MP.method: Either "classic" or "future". The former is the default and uses processx to execute multiple commands in parallel. When "future" the future.apply package is used for parallelization, which is especially useful for e.g. cluster computing.

  • patRoon.MP.futureSched: Sets the future.scheduling function argument for future_lapply. Only used if patRoon.MP.method="future".

  • patRoon.MP.logPath: The path used for logging of output from commands executed by multiprocess. Set to FALSE to disable logging.

  • patRoon.path.pwiz: The path in which the ProteoWizard binaries are installed. If unset an attempt is made to find this directory from the Windows registry and PATH environment variable.

  • patRoon.path.GenForm: The path to the GenForm executable. If not set (the default) the internal GenForm binary is used. Only set if you want to override the executable.

  • patRoon.path.MetFragCL: The complete file path to the MetFrag CL jar to be used by generateCompoundsMetFrag. Example: "C:/MetFrag2.4.2-CL.jar".

  • patRoon.path.MetFragCompTox: The complete file path to the CompTox database csv file. See generateCompounds for more details.

  • patRoon.path.MetFragPubChemLite: The complete file path to the PubChemLite database csv file. See generateCompounds for more details.

  • patRoon.path.SIRIUS: The directory in which the SIRIUS binaries are installed. Used by all functions that interface with SIRIUS, such as generateFormulasSIRIUS and generateCompoundsSIRIUS. Example: "C:/sirius-win64-3.5.1". Note that the location of the binaries differs for each operating system.

  • patRoon.path.OpenMS: The path in which the OpenMS binaries are installed.

  • patRoon.path.obabel: The path in which the OpenBabel binaries are installed.

  • patRoon.path.BiotransFormer The full file path to the biotransformer .jar command line utility. This needs to be set when generateTPsBioTransformer is used. For more details see https://bitbucket.org/djoumbou/biotransformer/src/master.

  • patRoon.path.limits A path to a customized limits YAML file.

Most external dependencies are provided by patRoonExt or otherwise found in the system environment PATH variable. However, the patRoon.path.* options should be set if this fails or you want to override the location. The verifyDependencies function can be used to assess if dependencies are found.

See also

Useful links:

Author

Maintainer: Rick Helmus r.helmus@uva.nl (ORCID)

Authors:

Other contributors:

  • Olaf Brock (ORCID) [contributor]

  • Vittorio Albergamo (ORCID) [contributor]

  • Andrea Brunner (ORCID) [contributor]

  • Emma Schymanski (ORCID) [contributor]

  • Bas van de Velde (ORCID) [contributor]

  • Leon Saal (ORCID) [contributor]