specDist.cosine-methods: a Distance function based on matching peaks
In xiaodfeng/DynamicXCMS: 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)