Generic adduct class

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

Usage

adduct(...)

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

# S4 method for class 'adduct'
as.character(x, format = "generic", adductInfo = NULL, 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.

"nontarget" is the format used by nontarget/enviPat and requires adductInfo to be set.

adductInfo

A data.frame with adduct info from e.g. enviPat::adducts. Only needs to be set when format="nontarget".

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).

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]+"

Usage

Arguments

Methods (by generic)

Slots

See also

Examples