adduct-class: Generic adduct class

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Generic adduct class

Description

Objects from this class are used to specify adduct information in an algorithm independent way.

Usage

adduct(...)

## S4 method for signature 'adduct'
show(object)

## S4 method for signature 'adduct'
as.character(x, format = "generic", err = TRUE)

Arguments

x, object	An adduct object.
format	A character that specifies the source format. "generic" is an internally used generic format that supports full textual conversion. Examples: "[M+H]+", "[2M+H]+", "[M+3H]3+". "sirius" Is the format used by SIRIUS. It is similar to generic but does not allow multiple charges/molecules. See the SIRIUS manual for more details. "genform" and "metfrag" support fixed types of adducts which can be obtained with the GenFormAdducts and MetFragAdducts functions, respectively. "openms" is the format used by the MetaboliteAdductDecharger tool. "cliquems" is the format used by cliqueMS.
err	If TRUE then an error will be thrown if conversion fails, otherwise returns without data.
...	Any of add, sub, molMult and/or charge. See ⁠Slots⁠.

Methods (by generic)

• show(adduct): Shows summary information for this object.

• as.character(adduct): Converts an adduct object to a specified character format.

Slots

add,sub

A character with one or more formulas to add/subtract.

molMult

How many times the original molecule is present in this molecule (e.g. for a dimer this would be ‘⁠2⁠’). Default is ‘⁠1⁠’.

charge

The final charge of the adduct (default ‘⁠1⁠’).

See Also

as.adduct for easy creation of adduct objects and adduct utilities for other adduct functionality.

Examples

adduct("H") # [M+H]+
adduct(sub = "H", charge = -1) # [M-H]-
adduct(add = "K", sub = "H2", charge = -1) # [M+K-H2]+
adduct(add = "H3", charge = 3) # [M+H3]3+
adduct(add = "H", molMult = 2) # [2M+H]+

as.character(adduct("H")) # returns "[M+H]+"

rickhelmus/patRoon documentation built on Nov. 22, 2024, 3:11 p.m.