selectPeaks: Select peaks from aggregate table

In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

Description

Selects peaks from aggregate table according to different criteria.

Usage

selectPeaks(o, ...)

## S4 method for signature 'RmbSpectrum2'
selectPeaks(o, filter, ..., enclos = parent.frame(2))

## S4 method for signature 'RmbSpectrum2List'
selectPeaks(o, ..., enclos = parent.frame(2))

## S4 method for signature 'RmbSpectraSetList'
selectPeaks(o, ..., enclos = parent.frame(2))

## S4 method for signature 'data.frame'
selectPeaks(o, filter, ..., enclos = parent.frame(2))

## S4 method for signature 'msmsWorkspace'
selectPeaks(o, ..., enclos = parent.frame(2))

## S4 method for signature 'RmbSpectrum2List,numeric,numeric'
cleanElnoise(
  peaks,
  noise = getOption("RMassBank")$electronicNoise,
  width = getOption("RMassBank")$electronicNoiseWidth
)

Arguments

o	msmsWorkspace or aggregate data.frame from a workspace.
...	no additional parameters
good	if TRUE, include good (matched within filter criteria) peaks.
bad	if TRUE, include bad (not matched within filter criteria) peaks. Note: good and bad can be combined, both are returned in that case.
cleaned	if TRUE, return only peaks which passed the noise filter. Note: If the noise filter was not applied, the parameter has no effect. Also, a noise column is in any case added to the output, even if not present before.
best	if TRUE, only select the best match for each peak (i.e. the formula with smallest delta ppm). Otherwise multiple matches can be returned.

Value

Peak dataframe according to the specified criteria.

Methods (by class)

• RmbSpectrum2: A method to filter spectra to the specified peaks

• RmbSpectrum2List: A method to filter spectra to the specified peaks

• RmbSpectraSetList: A method to filter spectra to the specified peaks

• data.frame: A method to retrieve the specified peaks from the "aggregated" slot (a data.frame object) in an msmsWorkSpace

• msmsWorkspace: A method to retrieve the specified peaks from an msmsWorkSpace

• peaks = RmbSpectrum2List,noise = numeric,width = numeric: A method to filter spectra to the specified peaks

Author(s)

stravsmi

sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.