| spectral_entropy_calculator {IDSL.FSA} | R Documentation |
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, 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]])