findFeaturesOpenMS: Find features using OpenMS

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Find features using OpenMS

Description

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

Usage

findFeaturesOpenMS(
  analysisInfo,
  noiseThrInt = 1000,
  chromSNR = 3,
  chromFWHM = 5,
  mzPPM = 10,
  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,
  intSearchRTWindow = 3,
  useFFMIntensities = FALSE,
  verbose = TRUE
)

Arguments

analysisInfo	A data.frame 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.
intSearchRTWindow	Retention time window (in seconds, +/- feature retention time) that is used to find the closest data point to the retention time to obtain the intensity of a feature (this is needed since OpenMS does not provide this data).
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.

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.

Value

An object of a class which is derived from features.

Parallelization

findFeaturesOpenMS 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.

References

\insertRef

Rst2016patRoon

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

\addCitationsRcpp1

\addCitationsRcpp2

\addCitationsRcpp3

See Also

findFeatures for more details and other algorithms.

rickhelmus/patRoon documentation built on Nov. 22, 2024, 3:11 p.m.