API feature finding module

Metabo Feature Finder

emzed.ff.runMetaboFeatureFinder(peak_map, config_id=None, ms_level=None, **kw)

calls pyopenms MassTraceDetection + FeatureFindingMetabo

following parameters can be passed after peakmap parameter:

Common Parameters:

  • common_noise_threshold_int: Intensity threshold below which peaks are regarded as noise. default value : 10.0 allowed values: -1.797693e+308..1.797693e+308
  • common_chrom_peak_snr: Minimum signal-to-noise a mass trace should have default value : 3.0 allowed values: -1.797693e+308..1.797693e+308
  • common_chrom_fwhm: Expected chromatographic peak width (in seconds). default value : 5.0 allowed values: -1.797693e+308..1.797693e+308

Parameters Mass Trace Detector:

  • mtd_mass_error_ppm: Allowed mass deviation (in ppm). default value : 20.0 allowed values: -1.797693e+308..1.797693e+308
  • mtd_reestimate_mt_sd: Enables dynamic re-estimation of m/z variance during mass trace collection stage. default value : ‘true’ allowed values: ‘true’, ‘false’
  • mtd_trace_termination_criterion: Termination criterion for the extension of mass traces. In ‘outlier’ mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In ‘sample_rate’ mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the ‘min_sample_rate’ threshold. default value : ‘outlier’ allowed values: ‘outlier’, ‘sample_rate’
  • mtd_trace_termination_outliers: Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached. default value : 5 allowed values: -2147483647..2147483647
  • mtd_min_sample_rate: Minimum fraction of scans along the mass trace that must contain a peak. default value : 0.5 allowed values: -1.797693e+308..1.797693e+308
  • mtd_min_trace_length: Minimum expected length of a mass trace (in seconds). default value : 5.0 allowed values: -1.797693e+308..1.797693e+308
  • mtd_max_trace_length: Minimum expected length of a mass trace (in seconds). default value : 300.0 allowed values: -1.797693e+308..1.797693e+308

Elution Peak Detection:

  • epdet_width_filtering: Enable filtering of unlikely peak widths. The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution. default value : ‘fixed’ allowed values: ‘off’, ‘fixed’, ‘auto’
  • epdet_min_fwhm: Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if paramter width_filtering is off or auto. default value : 3.0 allowed values: -1.797693e+308..1.797693e+308
  • epdet_max_fwhm: Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if paramter width_filtering is off or auto. default value : 60.0 allowed values: -1.797693e+308..1.797693e+308
  • epdet_masstrace_snr_filtering: Apply post-filtering by signal-to-noise ratio after smoothing. default value : ‘false’ allowed values: ‘false’, ‘true’

Parameters Feature Finding Metabo:

  • ffm_local_rt_range: RT range where to look for coeluting mass traces default value : 10.0 allowed values: -1.797693e+308..1.797693e+308
  • ffm_local_mz_range: MZ range where to look for isotopic mass traces default value : 6.5 allowed values: -1.797693e+308..1.797693e+308
  • ffm_charge_lower_bound: Lowest charge state to consider default value : 1 allowed values: -2147483647..2147483647
  • ffm_charge_upper_bound: Highest charge state to consider default value : 3 allowed values: -2147483647..2147483647
  • ffm_report_summed_ints: Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone. default value : ‘false’ allowed values: ‘false’, ‘true’
  • ffm_disable_isotope_filtering: Disable isotope filtering. default value : ‘false’ allowed values: ‘false’, ‘true’
  • ffm_isotope_model: Change type of isotope model. default value : ‘metabolites’ allowed values: ‘metabolites’, ‘peptides’
  • ffm_isotope_noisemodel: SVM isotope models were trained with either 2% or 5% RMS error. Select the appropriate noise model according to the quality of measurement or MS device. default value : ‘5%RMS’ allowed values: ‘5%RMS’, ‘2%RMS’
  • ffm_use_smoothed_intensities: Use LOWESS intensities instead of raw intensities. default value : ‘true’ allowed values: ‘false’, ‘true’

Centwave Feature Detector

emzed.ff.runCentwave(pm, **kws)[source]

runs centwave feature detector from XCMS on Peakmap pm.

For parameters see Docs from XCMS library

Matched Filter Feature Detector

emzed.ff.runMatchedFilters(pm, **kws)[source]

runs matched filters feature detector from XCMS on Peakmap pm.

For parameters see Docs from XCMS library