getSimilarities {CluMSID} | R Documentation

## Match one spectrum against a set of spectra

### Description

`getSimilarities` calculates the similarities of one spectrum or neutral loss pattern to a set of other spectra or neutral loss patterns.

### Usage

    getSimilarities(spec, speclist, type = c("spectrum", "neutral_losses"),
        hits_only = FALSE)

### Arguments

`spec` | The spectrum to be compared to other spectra. Can be either an object of class `MS2spectrum` or a two-column numerical matrix that contains fragment mass-to-charge ratios in the first and intensities in the second column.
`speclist` | The set of spectra to which `spec` is to be compared. Must be a list where every entry is an object of class `MS2spectrum`. Can be generated from an mzXML file with `extractMS2spectra` and `mergeMS2spectra` or constructed using `new("MS2spectrum", ...)` for every list entry (see vignette for details).
`type` | Specifies whether MS2 spectra or neutral loss patterns are to be compared. Must be either `'spectrum'` (default) or `'neutral_losses'`.
`hits_only` | Logical that indicates whether the result should contain only similarities greater than zero.

### Value

A named vector with similarities of `spec` to all spectra or neutral loss patterns in `speclist`.

### Examples

    load(file = system.file("extdata",
        "annotatedSpeclist.RData",
        package = "CluMSIDdata"))
    getSimilarities(annotatedSpeclist[[137]],
                    annotatedSpeclist, hits_only = TRUE)

[Package CluMSID version 1.3.1 Index]