specDist.cosine {xcms} | R Documentation

## 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

### 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.

### 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)`

### Author(s)

Joachim Kutzera, jkutzer@ipb-halle.de

[Package xcms version 3.10.2 Index]