MS2spectrum-class: A custom S4 class for MS2 spectra, neutral loss patterns and...

In tdepke/CluMSID: Clustering of MS2 Spectra for Metabolite Identification

A custom S4 class for MS2 spectra, neutral loss patterns and respective metainformation

Description

A custom S4 class for MS2 spectra, neutral loss patterns and respective metainformation

Usage

## S4 method for signature 'MS2spectrum'
show(object)

## S4 method for signature 'MS2spectrum'
precursorMz(object)

## S4 method for signature 'MS2spectrum'
rtime(object)

## S4 method for signature 'MS2spectrum'
intensity(object)

## S4 method for signature 'MS2spectrum'
mz(object)

## S4 method for signature 'MS2spectrum,ANY'
peaksCount(object)

Arguments

object

An object of class MS2spectrum

Value

Prints information from the object slots with exception of 'spectrum' and 'neutral_losses' where only a summary is given.

Methods (by generic)

• show: A show generic for MS2spectra.

• precursorMz: Method forMSnbase::precursorMz for MS2spectrum objects. Accesses precursor slot and returns precursor m/z as a numeric.

• rtime: Method forMSnbase::rtime for MS2spectrum objects. Accesses rt slot and returns retention time as a numeric.

• intensity: Method forMSnbase::intensity for MS2spectrum objects. Accesses spectrum slot and returns the intensity column as a numeric vector.

• mz: Method forMSnbase::mz for MS2spectrum objects. Accesses spectrum slot and returns the m/z column as a numeric vector.

• peaksCount: Method forMSnbase::mz for MS2spectrum objects. Accesses spectrum slot and returns the number of peaks as a numeric.

Slots

id

a character string similar to the ID used by XCMSonline or the ID given in a predefined peak list

annotation

a character string containing a user-defined annotation, defaults to empty

precursor

(median) m/z of the spectrum's precursor ion

rt

(median) retention time of the spectrum's precursor ion

polarity

the ionisation polarity, "positive" or "negative"

spectrum

the actual MS2 spectrum as two-column matrix (column 1 is (median) m/z, column 2 is (median) intensity of the product ions)

neutral_losses

a neutral loss pattern generated by subtracting the product ion mass-to-charge ratios from the precursor m/z in a matrix format analogous to the spectrum slot

tdepke/CluMSID documentation built on April 10, 2022, noon