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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/entropy.R |
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+\name{entropy}
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+\alias{entropy}
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+\title{Spectral entropy}
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+\usage{
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+entropy(x) |
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+} |
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+\arguments{
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+\item{x}{\code{numeric}, intensities of the fragment ions.}
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+} |
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+\value{
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+\code{numeric}: (normalized) entropy \code{x}.
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+} |
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+\description{
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+These functions allow to calculate entropy measurements of an MS/MS |
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+spectrum based on the metrics suggested by |
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+Li et al. (https://doi.org/10.1038/s41592-021-01331-z). |
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+Spectral entropy and normalized entropy are used to measure the complexity |
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+of an spectra. |
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+MassBank of North America (MoNA) defines spectra entropy as the intensity |
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+weighted spectral peak number |
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+(https://mona.fiehnlab.ucdavis.edu/documentation/entropy. |
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+Additionally it is suggested to label as low-quality spectrums the ones |
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+that have a normalized entropy higher than 0.8 and spectral entropy |
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+higher than 3. |
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+} |
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+\examples{
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+spectrum <- rbind(c(41.04, 37.16), c(69.07, 66.83), c(86.1, 999.0)) |
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+ |
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+entropy(spectrum[,2]) |
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+nentropy(spectrum[,2]) |
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+ |
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+} |
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+\author{
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+Mar Garcia-Aloy |
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+} |
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+\concept{helper functions for users
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+ |
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+#' @references |
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+Li, Y., Kind, T., Folz, J., Vaniya, A., Mehta. S.S., Fiehn, O. (2021). |
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+Spectral entropy outperforms MS/MS dot product similarity for |
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+small-molecule compound identification. |
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+Nature Methods. 2021;18(12):1524-1531. |
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+\doi{10.1038/s41592-021-01331-z}.}
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