Find features using OpenMS

uses the FeatureFinderMetabo TOPP tool (see http://www.openms.de) to find features.

Usage

findFeaturesOpenMS(
  analysisInfo,
  noiseThrInt = 1000,
  chromSNR = 3,
  chromFWHM = 5,
  mzPPM = defaultLim("mz", "medium_rel"),
  reEstimateMTSD = TRUE,
  traceTermCriterion = "sample_rate",
  traceTermOutliers = 5,
  minSampleRate = 0.5,
  minTraceLength = 3,
  maxTraceLength = -1,
  widthFiltering = "fixed",
  minFWHM = 1,
  maxFWHM = 30,
  traceSNRFiltering = FALSE,
  localRTRange = 10,
  localMZRange = 6.5,
  isotopeFilteringModel = "metabolites (5% RMS)",
  MZScoring13C = FALSE,
  useSmoothedInts = TRUE,
  extraOpts = NULL,
  useFFMIntensities = FALSE,
  verbose = TRUE
)

Arguments

analysisInfo: A data.frame (or data.table) with Analysis information.
noiseThrInt: Noise intensity threshold. Sets algorithm:common:noise_threshold_int option.
chromSNR: Minimum S/N of a mass trace. Sets algorithm:common:chrom_peak_snr option.
chromFWHM: Expected chromatographic peak width (in seconds). Sets algorithm:common:chrom_fwhm option.
mzPPM: Allowed mass deviation (ppm) for trace detection. Sets algorithm:mtd:mass_error_ppm.
reEstimateMTSD: If TRUE then enables dynamic re-estimation of m/z variance during mass trace collection stage. Sets algorithm:mtd:reestimate_mt_sd.
traceTermCriterion, traceTermOutliers, minSampleRate: Termination criterion for the extension of mass traces. See FeatureFinderMetabo. Sets the algorithm:mtd:trace_termination_criterion, algorithm:mtd:trace_termination_outliers and algorithm:mtd:min_sample_rate options, respectively.
minTraceLength, maxTraceLength: Minimum/Maximum length of mass trace (seconds). Set negative value for maxlength to disable maximum. Sets algorithm:mtd:min_trace_length and algorithm:mtd:min_trace_length, respectively.
widthFiltering, minFWHM, maxFWHM: Enable filtering of unlikely peak widths. See FeatureFinderMetabo. Sets algorithm:epd:width_filtering, algorithm:epd:min_fwhm and algorithm:epd:max_fwhm, respectively.
traceSNRFiltering: If TRUE then apply post-filtering by signal-to-noise ratio after smoothing. Sets the algorithm:epd:masstrace_snr_filtering option.
localRTRange, localMZRange: Retention/MZ range where to look for coeluting/isotopic mass traces. Sets the algorithm:ffm:local_rt_range and algorithm:ffm:local_mz_range options, respectively.
isotopeFilteringModel: Remove/score candidate assemblies based on isotope intensities. See FeatureFinderMetabo. Sets the algorithm:ffm:isotope_filtering_model option.
MZScoring13C: Use the 13C isotope as the expected shift for isotope mass traces. See FeatureFinderMetabo. Sets algorithm:ffm:mz_scoring_13C.
useSmoothedInts: If TRUE then use LOWESS intensities instead of raw intensities. Sets the algorithm:ffm:use_smoothed_intensities option.
extraOpts: Named list containing extra options that will be passed to FeatureFinderMetabo. Any options specified here will override any of the above. Example: extraOpts=list("-algorithm:common:noise_threshold_int"=1000) (corresponds to setting noiseThrInt=1000). Set to NULL to ignore.
useFFMIntensities: If TRUE then peak intensities are directly loaded from FeatureFinderMetabo output. Otherwise, intensities are loaded afterwards from the input mzML files, which is potentially much slower, especially with many analyses files. However, useFFMIntensities=TRUE is still somewhat experimental, may be less accurate and requires a recent version of OpenMS (>=2.7).
verbose: If set to FALSE then no text output is shown.

Value

An object of a class which is derived from features.

Details

This function uses OpenMS to automatically find features. This function is called when calling findFeatures with algorithm="openms".

This functionality has been tested with OpenMS version >= 2.0. Please make sure it is installed and configured, e.g. by installing patRoonExt or configuring the path of the binaries with the patRoon.path.OpenMS option or the system PATH variable.

The file format of analyses must be mzML.

The input MS data files need to be centroided. The convertMSFiles function can be used to centroid data.

Parallelization

findFeaturesOpenMS with useFFMIntensities=FALSE uses multiprocessing to parallelize computations. Please see the parallelization section in the handbook for more details and patRoon options for configuration options.

Note that for caching purposes, the analyses files must always exist on the local host computer, even if it is not participating in computations.

Use of raw HRMS data

The raw data interface of patRoon is used by findFeaturesOpenMS with useFFMIntensities=FALSE to process HRMS (or IMS-HRMS) data. Please see its documentation for more information on the supported formats and available configuration options.

References

Rost HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich H, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmstrom L, Aebersold R, Reinert K, Kohlbacher O (2016). “OpenMS: a flexible open-source software platform for mass spectrometry data analysis.” Nature Methods, 13(9), 741–748. doi:10.1038/nmeth.3959 .

pugixml (via Rcpp) is used to process OpenMS XML output.

Eddelbuettel D (2013). Seamless R and C++ Integration with Rcpp. Springer, New York. doi:10.1007/978-1-4614-6868-4 . ISBN 978-1-4614-6867-7.

Eddelbuettel D, Balamuta J (2018). “Extending R with C++: A Brief Introduction to Rcpp.” The American Statistician, 72(1), 28-36. doi:10.1080/00031305.2017.1375990 .

Eddelbuettel D, François R (2011). “Rcpp: Seamless R and C++ Integration.” Journal of Statistical Software, 40(8), 1–18. doi:10.18637/jss.v040.i08 .

Eddelbuettel D, Francois R, Allaire J, Ushey K, Kou Q, Russell N, Ucar I, Bates D, Chambers J (2026). Rcpp: Seamless R and C++ Integration. R package version 1.1.2, https://www.rcpp.org.