Parameters relevant for calculation of similarities between mass spectra.
getDefSpecSimParams(...)optional named arguments that override defaults.
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.
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.