calc_aroma: Calculate Aromaticity and Modified Aromaticity Values

In EMSL-Computing/fticRanalysis: Analysis and visualization tools for FT-MS data

Calculate Aromaticity and Modified Aromaticity Values

Description

Calculate aromaticity and modified aromaticity index values for peaks where empirical formula is available

Usage

calc_aroma(ftmsObj)

Arguments

ftmsObj

an object of class 'peakData' or 'compoundData', typically a result of as.peakData or mapPeaksToCompounds.

Details

AI = \frac{1 + C - O - S - 0.5(N + P + H)}{C - O - S - N - P} and AI_MOD = \frac{1 + C - 0.5O - S - 0.5(N + P + H)}{C - 0.5*O - S - N - P}. When the numerator or denominator is <=0, AI and AI_MOD = 0. When AI > 0.5 a compound is considered not aromatic, 0.5 < = AI <0.67 a compound is aromatic, and when AI >= 0.67 a compound is a condensed aromatic

Value

an object of the same class as ftmsObj with a column in e\_meta giving aromaticity and modified aromaticity values

Author(s)

Lisa Bramer

References

Koch, B. P., & Dittmar, T. (2006). From mass to structure: an aromaticity index for high‐resolution mass data of natural organic matter. Rapid communications in mass spectrometry, 20(5), 926-932.

Errata: Koch, B. P., & Dittmar, T. (2016). From mass to structure: an aromaticity index for high-resolution mass data of natural organic matter. Rapid communications in mass spectrometery, 30(1), 250. DOI: 10.1002/rcm.7433

EMSL-Computing/fticRanalysis documentation built on Dec. 18, 2024, 9:51 p.m.