cossim {CluMSID} | R Documentation

## Calculate cosine similarity between two spectra

### 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]])

[Package CluMSID version 1.0.0 Index]