spectral_entropy_calculator: Spectral Entropy Calculator

In IDSL.FSA: Fragmentation Spectra Analysis (FSA)

Spectral Entropy Calculator

Description

This module calculates spectral entropy for a fragmentation pattern using a method described by the reference paper.

Usage

spectral_entropy_calculator(FragmentList, allowedWeightedSpectralEntropy = TRUE,
noiseRemovalRatio = 0.01)

Arguments

FragmentList	A matrix (m/z, int) of fragmentation pattern after intensity adjustment
allowedWeightedSpectralEntropy	c(TRUE, FALSE). Weighted entropy to transform low abundant signals prior to calculating entropy similarity score. Please see the reference for details on weight transformation.
noiseRemovalRatio	noise removal ratio ([0 - 1])relative to the basepeak to measure entropy similarity score.

Value

spectralEntropy	spectral entropy
NumPeaks	NumPeaks
FragmentList	A matrix of two-columns after intensity normalization relative to summation of intensities AND entropy weight transformation when is selected.

Note

noise removal on intensities should be performed prior to feeding to this function

References

Li, Y., Kind, T., Folz, J., Vaniya, A., Mehta, S.S. and Fiehn, O. (2021). Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification. Nature methods, 18(12), 1524-1531, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41592-021-01331-z")}

Examples

FragmentList <- cbind(seq(50, 600, length.out = 10), seq(10, 90, length.out = 10))
SE <- spectral_entropy_calculator(FragmentList)
print(SE[[1]])

IDSL.FSA documentation built on July 9, 2023, 6:45 p.m.