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xcms (version 1.48.0)

specDist.cosine: a Distance function based on matching peaks

Description

This method calculates the distance of two sets of peaks using the cosine-distance.

Usage

specDist.cosine(peakTable1, peakTable2, mzabs=0.001, mzppm=10, mzExp=0.6, intExp=3, nPdiff=2, nPmin=8, symmetric=FALSE)

Arguments

peakTable1
a Matrix containing at least m/z-values, row must be called "mz"
peakTable2
the matrix for the other mz-values
mzabs
maximum absolute deviation for two matching peaks
mzppm
relative deviations in ppm for two matching peaks
symmetric
use symmetric pairwise m/z-matches only, or each match
mzExp
the exponent used for mz
intExp
the exponent used for intensity
nPdiff
the maximum nrow-difference of the two peaktables
nPmin
the minimum absolute sum of peaks from both praktables

Methods

peakTable1 = "matrix", peakTable2 = "matrix"
specDist.cosine(peakTable1, peakTable2, mzabs = 0.001, mzppm = 10, mzExp = 0.6, intExp = 3, nPdiff = 2, nPmin = 8, symmetric = FALSE)

Details

The result is the cosine-distance of the product from weighted factors of mz and intensity from matching peaks in the two peaktables. The factors are calculated as wFact = mz^mzExp * int^intExp. if no distance is calculated (for example because no matching peaks were found) the return-value is NA.