addAd: addAd

In RogerGinBer/RHermes: Improving metabolome characterization using molecular formula databases

addAd

Description

Adds new custom adducts to the RHermesExp adduct list

Usage

addAd(struct, name, deltam, ch = 1, mult = 1, toadd = "FALSE", tosub = "FALSE")

## S4 method for signature 'RHermesExp,character,numeric'
addAd(struct, name, deltam, ch = 1, mult = 1, toadd = "FALSE", tosub = "FALSE")

Arguments

struct	The RHermesExp object
name	Name of the adduct to add.
deltam	Delta m/z of the adduct, in Da.
ch	Adduct charge. Remember to specify the symbol if negative.
mult	Multiplicity (eg, M, 2M, 3M, etc.)
toadd	Atoms to add to the formula when it ionizes as the adduct. (ex: M+H -> H1, M+Cl -> Cl1). Note the explicit use of a 1 after the symbol.
tosub	Atoms to substract to the formula. Same idea as in toadd. (ex: M-H2O+H -> H2O1)

Details

The function adds an entry to the Envipat-style dataframe containing the adducts used for the experiment. It is important to specify what atoms to add or substract to the molecular formula. Polarity is inferred directly from the specified charge.

Value

An updated RHermesExp object with the new adduct list

Examples

if(FALSE){
 addAd(myHermes, 'M+H', 1.0072, ch = 1, mult = 1, toadd = 'H1')
}

RogerGinBer/RHermes documentation built on Nov. 6, 2022, 11:34 a.m.