normalizeddotproduct {MetCirc} | R Documentation

## Calculate the normalized dot product

### Description

Calculate the normalized dot product (NDP)

### Usage

    normalizeddotproduct(x, y, m=0.5, n=2, ...)

### Arguments

`x` | `Spectrum2` object from `MSnbase` containing intensity and m/z values, first MS/MS spectrum
`y` | `Spectrum2` object from `MSnbase` containing intensity and m/z values, second MS/MS spectrum
`m` | `numeric`, exponent to calculate peak intensity-based weights
`n` | `numeric`, exponent to calculate m/z-based weights
`...` | further arguments passed to MSnbase:::bin_Spectra

### Details

The normalized dot product is calculated according to the following formula:

∑(W_{S1, i} \cdot W_{S2, i}) ^ 2 ∑(W_{S1, i} ^ 2) * ∑(W_{S2, i} ^ 2)

, with W = [ peak intensity] ^{m} \cdot [m/z]^n. For further information see Li et al. (2015): Navigating natural variation in herbivory-induced secondary metabolism in coyote tobacco populations using MS/MS structural analysis. PNAS, E4147–E4155. `normalizeddotproduct` returns a numeric value ranging between 0 and 1, where 0 indicates no similarity between the two MS/MS features, while 1 indicates that the MS/MS features are identical. Arguments can be passed to the function `MSnbase:::bin_Spectra`, e.g. to set the width of bins (binSize). Prior to calculating

W_{S1}

or

W_{S2}

, all intensity values are divided by the maximum intensity value.

### Value

normalizeddotproduct returns a numeric similarity coefficient between 0 and 1

### Author(s)

Thomas Naake, thomasnaake@googlemail.com

### Examples

    data("spectra", package="MetCirc")
    x <- spectra_tissue[[1]]
    y <- spectra_tissue[[2]]
    normalizeddotproduct(x, y, m=0.5, n=2, binSize=0.01)

[Package MetCirc version 1.18.0 Index]