distanceMatrix: Create distance matrix from list of spectra

In tdepke/CluMSID: Clustering of MS2 Spectra for Metabolite Identification

Create distance matrix from list of spectra

Description

distanceMatrix() creates a distance matrix from a list of MS2 spectra, MS1 pseudospectra or neutral loss patterns by pairwise comparison using the specified distance function. This distance matrix is the basis for CluMSID's data mining functions.

Usage

distanceMatrix(speclist, distFun = "cossim", type = c("spectrum",
    "neutral_losses"), mz_tolerance = 1e-05)

Arguments

speclist	A list of MS2spectrum or pseudospectrum objects as generated by extractMS2spectra or extractPseudospectra.
distFun	The distance function to be used. At the moment, only cossim is implemented.
type	"spectrum" (default) for MS2 spectra or MS1 pseudospectra or "neutral_losses" for neutral loss patterns.
mz_tolerance	The m/z tolerance to be used for merging, default is 1e-5, i.e. +/- 10ppm. If the mass-to-charge ratios of two peaks differ less than mz_tolerance, they are assumed to have the same m/z

Value

A numeric length(speclist) by length(speclist) matrix containing pairwise distances (1 - similarity) between all features in speclist. Row and column names are taken from the id slot or, if present, pasted from the id and annotation slots of the MS2spectrum or pseudospectrum objects.

Examples

load(file = system.file("extdata",
    "annotatedSpeclist.RData",
    package = "CluMSIDdata"))

distanceMatrix(annotatedSpeclist[1:20])

tdepke/CluMSID documentation built on April 10, 2022, noon