compute_arom_index: compute_arom_index

In robertyoung3/MSanalyzeNOM: Utilities for Analyzing Complex Natural Organic Matter (NOM) Mixtures After Formula Assignment

Description

This function is designed to compute the aromaticity index (AI) or modified aromaticity index (ModAI) for the assigned molecular formulas in an MS dataset. The calclulations are derived from Koch and Dittmar 2006 (http://dx.doi.org/10.1002/rcm.2386) with erratum (http://dx.doi.org/10.1002/rcm.7433). The ModAI calculation treats one-half of the oxygen as carboxyl oxygen, rather than carbonyl oxygen, in line with published NMR data on marine DOM. This increases the number of compounds that qualify as aromatic or condensed aromatic, but is still more conservative than RDBE/C ratios. A (modified) aromaticity index >= 0.5 indicates an aromatic structure, and a (modified) aromaticity index >= 0.67 indicates a condensed aromatic structure.

Usage

compute_arom_index(df, elements = c("C", "H", "N", "O", "S"), AItype = "ModAI")

Arguments

df	a tibble containing a table of the assigned elements with a column name for each element (e.g., "C", "H", "N", "O" and "S")
elements	a character vector of the elements used for formula assignment (default = CHNOS)
AItype	a character string where "AI" = aromaticity index or "ModAI" = modified aromaticity index

Value

a vector containing the aromaticity index for every assigned formula

robertyoung3/MSanalyzeNOM documentation built on June 7, 2021, 7:46 a.m.