cossim: Calculate cosine similarity between two spectra

In CluMSID: Clustering of MS2 Spectra for Metabolite Identification

Description

cossim() calculates the cosine of the spectral constrast angle as a measure for the similarity of two spectra.

Usage

cossim(x, y, type = c("spectrum", "neutral_losses"),
    mzTolerance = 1e-05)

## S4 method for signature 'MS2spectrum,MS2spectrum'
cossim(x, y, type = c("spectrum",
    "neutral_losses"), mzTolerance = 1e-05)

## S4 method for signature 'pseudospectrum,pseudospectrum'
cossim(x, y,
    type = c("spectrum", "neutral_losses"), mzTolerance = 1e-05)

Arguments

x, y	MS2 spectra, either as matrix, MS2spectrum or pseudospectrum objects. x and y must have the same class.
type	Whether similarity between spectra ("spectrum", default) or neutral loss patterns ("neutral_losses") is to be compared
mzTolerance	The m/z tolerance used for merging. If two fragment peaks are within tolerance, they are regarded as the same. Defaults to 1e-5, i.e. 10ppm.

Value

The cosine similarity of x and y

Methods (by class)

• x = MS2spectrum,y = MS2spectrum: cossim method for MS2spectrum objects

• x = pseudospectrum,y = pseudospectrum: cossim method for pseudospectrum objects

Examples

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

cossim(annotatedSpeclist[[1]], annotatedSpeclist[[2]])

CluMSID documentation built on Nov. 8, 2020, 7:46 p.m.