MassSpecMethod_GenerateFormulas_genform S7 class — MassSpecMethod_GenerateFormulas

Settings for generating formulas using the algorithm GenForm. The algorithm is used via the function generateFormulas from the package patRoon. Therefore, it is highly recommended to check the original documentation of the function in patRoon for more details.

Usage

MassSpecMethod_GenerateFormulas_genform(
  MSPeakListsClusterMzWindow = 0.005,
  MSPeakListsTopMost = 100,
  MSPeakListsMinIntensityPre = 50,
  MSPeakListsMinIntensityPost = 50,
  MSPeakListsAvgFun = "mean",
  MSPeakListsMethod = "distance",
  relMzDev = 5,
  elements = "CHNOP",
  hetero = TRUE,
  oc = FALSE,
  thrMS = numeric(),
  thrMSMS = numeric(),
  thrComb = numeric(),
  maxCandidates = Inf,
  extraOpts = character(),
  calculateFeatures = TRUE,
  featThreshold = 0,
  featThresholdAnn = 0.75,
  absAlignMzDev = 0.002,
  MSMode = "both",
  isolatePrec = TRUE,
  timeout = 120,
  topMost = 50,
  batchSize = 8
)

Arguments

MSPeakListsClusterMzWindow: m/z window (in Da) used for clustering m/z values when spectra are averaged. For method="hclust" this corresponds to the cluster height, while for method="distance" this value is used to find nearby masses (+/- window). Too small windows will prevent clustering m/z values (thus erroneously treating equal masses along spectra as different), whereas too big windows may cluster unrelated m/z values from different or even the same spectrum together.
MSPeakListsTopMost: Only retain this maximum number of MS peaks when generating averaged spectra. Lowering this number may exclude more irrelevant (noisy) MS peaks and decrease processing time, whereas higher values may avoid excluding lower intense MS peaks that may still be of interest.
MSPeakListsMinIntensityPre: MS peaks with intensities below this value will be removed (applied prior to selection by topMost) before averaging.
MSPeakListsMinIntensityPost: MS peaks with intensities below this value will be removed after averaging.
MSPeakListsAvgFun: Character with the function name that is used to calculate average m/z values.
MSPeakListsMethod: Method used for producing averaged MS spectra. Valid values are "hclust", used for hierarchical clustering (using the fastcluster package), and "distance", to use the between peak distance. The latter method may reduces processing time and memory requirements, at the potential cost of reduced accuracy.
relMzDev: Numeric (length 1) with the relative mass deviation, in ppm.
elements: Character vector with the elements to use for formulae annotation. Always try to work with a minimal set by excluding elements you don't expect.
hetero: Logical (length 1) indicating if heteroatoms are allowed in the formulae.
oc: Logical (length 1) indicating presence of at least one carbon in the formulae.
thrMS: Numeric (length 1) Sets the thresholds for the GenForm MS score (isoScore). Sets the thms command line options, respectively. Set to NULL for no threshold.
thrMSMS: Numeric (length 1) Sets the thresholds for the GenForm MS/MS score (MSMSScore). Sets the thmsms command line options, respectively. Set to NULL for no threshold.
thrComb: Numeric (length 1) Sets the thresholds for the GenForm combined score (combMatch). Sets the thcomb command line options, respectively. Set to NULL for no threshold.
maxCandidates: Numeric (length 1) with the maximum number of candidates to be generated.
extraOpts: Character (length 1) with extra CLI options to be passed to the GenForm algorithm.
calculateFeatures: Logical (length 1) indicating if features should be calculated.
featThreshold: Numeric (length 1). If calculateFeatures is TRUE the minimum presence (from 0 to 1) of features with formula annotation to be considered for the respective feature group.
featThresholdAnn: Numeric (length 1). As featThreshold, but only considers features with annotations.
absAlignMzDev: Numeric (length 1). When the group formula annotation consensus is made from feature annotations, the m/z values of annotated MS/MS fragments may slightly deviate from those of the corresponding group MS/MS peak list. The absAlignMzDev argument specifies the maximum m/z window used to re-align the mass peaks.
MSMode: Character (length 1) with the MS mode to be used. Possible values are "MS", "MSMS", or "both".
isolatePrec: Settings used for isolation of precursor mass peaks and their isotopes. This isolation is highly important for accurate isotope scoring of candidates, as non-relevant mass peaks will dramatically decrease the score. The value of isolatePrec should either be a list with parameters (see the filter method for MSPeakLists for more details), TRUE for default parameters or FALSE for no isolation (e.g. when you already performed isolation with the filter method). The z parameter (charge) is automatically deduced from the adduct used for annotation (unless isolatePrec is FALSE), hence any custom z setting is ignored.
timeout: Numeric (length 1) with the maximum time in seconds to wait for the GenForm algorithm to finish.
topMost: Numeric (length 1) with the maximum number of top candidates to be returned.
batchSize: Maximum number of GenForm commands that should be run sequentially in each parallel process.

Value

A MassSpecMethod_GenerateFormulas_genform object.

References

Helmus R, ter Laak TL, van Wezel AP, de Voogt P, Schymanski EL (2021). “patRoon: open source software platform for environmental mass spectrometry based non-target screening.” Journal of Cheminformatics, 13(1). doi:10.1186/s13321-020-00477-w .

Helmus R, van de Velde B, Brunner AM, ter Laak TL, van Wezel AP, Schymanski EL (2022). “patRoon 2.0: Improved non-target analysis workflows including automated transformation product screening.” Journal of Open Source Software, 7(71), 4029. doi:10.21105/joss.04029 .

Meringer M, Reinker S, Zhang J, Muller A (2011). “MS/MS data improves automated determination of molecular formulas by mass spectrometry.” MATCH Commun. Math. Comput. Chem, 65(2), 259–290.