adductFormula: Calculate a table of adduct (ionic) formulas

In rformassspectrometry/MetaboCoreUtils: Core Utils for Metabolomics Data

Calculate a table of adduct (ionic) formulas

Description

adductFormula calculates the chemical formulas for the specified adducts of provided chemical formulas.

Usage

adductFormula(formulas, adduct = "[M+H]+", standardize = TRUE)

Arguments

formulas	character with molecular formulas for which adduct formulas should be calculated.
adduct	character or data.frame of valid adduct. to be used. Custom adduct definitions can be provided via a data.frame but its format must follow adducts()
standardize	logical(1) whether to standardize the molecular formulas to the Hill notation system before calculating their mass.

Value

character matrix with formula rows and adducts columns containing all ion formulas. In case an ion can't be generated (eg. [M-NH3+H]+ in a molecule that doesn't have nitrogen), a NA is returned instead.

Author(s)

Roger Gine

See Also

adductNames() for a list of all available predefined adducts and adducts() for the adduct data.frame definition style.

Examples

# Calculate the ion formulas of glucose with adducts [M+H]+, [M+Na]+ and [M+K]+
adductFormula("C6H12O6", c("[M+H]+", "[M+Na]+", "[M+K]+"))

# > "[C6H13O6]+" "[C6H12O6Na]+" "[C6H12O6K]+"

# Use a custom set of adduct definitions (For instance, a iron (Fe2+) adduct)
custom_ads <- data.frame(name = "[M+Fe]2+", mass_multi = 0.5, charge = 2,
                         formula_add = "Fe", formula_sub = "C0",
                         positive = "TRUE")
adductFormula("C6H12O6", custom_ads)

rformassspectrometry/MetaboCoreUtils documentation built on Oct. 2, 2024, 5:13 a.m.