# specDist.cosine-methods: a Distance function based on matching peaks In sneumann/xcms: LC-MS and GC-MS Data Analysis

 specDist.cosine 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

sneumann/xcms documentation built on June 5, 2024, 4:28 p.m.