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MS spectral similarity calculation parameters

Source: R/utils-mspeaklists.R
specSimParams.Rd

Parameters relevant for calculation of similarities between mass spectra.

Usage

getDefSpecSimParams(...)

Arguments

...

optional named arguments that override defaults.

Details

For the calculation of spectral similarities the following parameters exist:

  • method The similarity method: either "cosine" or "jaccard".

  • removePrecursor If TRUE then precursor peaks (i.e. the mass peak corresponding to the feature) are removed prior to similarity calculation.

  • mzWeight,intWeight Mass and intensity weights used for cosine calculation.

  • absMzDev Maximum absolute m/z deviation between mass peaks, used for binning spectra. Defaults to defaultLim("mz", "medium") (see limits).

  • relMinIntensity The minimum relative intensity for mass peaks (0-1). Peaks with lower intensities are not considered for similarity calculation. The relative intensities are called after the precursor peak is removed when removePrecursor=TRUE.

  • minPeaks Only consider spectra that have at least this amount of peaks (after the spectrum is filtered).

  • shift If and how shifting is applied prior to similarity calculation. Valid options are: "none" (no shifting), "precursor" (all mass peaks of the second spectrum are shifted by the mass difference between the precursors of both spectra) or "both" (the spectra are first binned without shifting, and peaks still unaligned are then shifted as is done when shift="precursor").

  • setCombinedMethod (sets workflow) Determines how spectral similarities from different sets are combined. Possible values are "mean", "min" or "max", which calculates the combined value as the mean, minimum or maximum value, respectively. NA values (e.g. if a set does not have peak list data to combine) are removed in advance.

These parameters are typically passed as a named list as the specSimParams argument to functions that do spectral similarity calculations. The getDefSpecSimParams function can be used to generate such parameter list with defaults.