isotopicSubstitutionMatrix {MetaboCoreUtils}R Documentation

Definitions of isotopic substitutions

Description

In order to identify potential isotopologues based on only m/z and intensity values with the isotopologues() function, sets of pre-calculated parameters are required. This function returns such parameter sets estimated on different sources/databases. The nomenclature used to describe isotopes follows the following convention: the number of neutrons is provided in [ as a prefix to the element and the number of atoms of the element as suffix. [13]C2[37]Cl3 describes thus an isotopic substitution containing 2 [13]C isotopes and 3 [37]Cl isotopes.

Each row in the returned data.frame characterizes an isotopic substitution (which can involve isotopes of several elements or different isotopes of the same element). The provided isotopic substitutions are in general the most frequently observed substitutions in the database (e.g. HMDB) on which they were defined. Parameters (columns) defined for each isotopic substitution are:

Usage

isotopicSubstitutionMatrix(source = c("HMDB"))

Arguments

source

character(1) defining the set of predefined parameters and isotopologue definitions to return.

Value

data.frame with parameters to detect the defined isotopic substitutions

Available pre-calculated substitution matrices

Author(s)

Andrea Vicini

Examples


## Get the substitution matrix calculated on HMDB
isotopicSubstitutionMatrix("HMDB")

[Package MetaboCoreUtils version 1.1.1 Index]