RHermesPL-class: RHermesPL

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

RHermesPL

Description

The RHermesPL class contains all the annotation details from a single MS1 mzML file, as well as some raw information that is useful for other steps of the workflow. RHermesPL objects are generated by processMS1 and should not be declared manually.

Usage

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

Arguments

object

An RHermesPL object

Value

An RHermesPL object

Slots

peaklist

Data.table containing all annotated data points. It stores, rt values, mz, intensities, ionic formulas and isotope annotations.

header

Dataframe with headers from the mzML file. Extracted with mzR::header() and filtered empty scans (if any).

raw

Dataframe of raw data points from the mzML file. Extracted with mzR::peaks() and filtered by the noise parameter from ExpParam.

labelled

Logical. Whether all possible 13C isotopologues were searched for in the data. Usually FALSE, only TRUE if you're dealing with 13C labelled data. Should not be set by the user here. Instead, tell processMS1 using labelled = TRUE.

filename

Filename of the original mzML file.

Author(s)

Roger Gine

See Also

processMS1 ExpParam

Other Containers: RHermesIL-class, RHermesMS2Exp-class, RHermesSOI-class

Examples

PL(struct, 1) #Access the object using the getter function.

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