group.FIA-proFIAset-method: Group the peaks of an FIA acquisition.

Description Usage Arguments Value Examples

Description

Group the peaks in a FIA experiemnts by clustering under an estimated density based on the accuracy in ppm of the mass spectrometer.

Usage

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## S4 method for signature 'proFIAset'
group.FIA(object, ppmGroup, solvar = FALSE, sleep = 0,
  dmzGroup = 5e-04, fracGroup = 0.5)

Arguments

object

A proFIAset object.

ppmGroup

A ppm parameter giving the size of the windows considered, we recommend to use 0.5*ppm where ppm is the pp parameter of band detection in the proFIAset function.

solvar

Shall the group corresponding to solvent signal be kept. This in only useful if solvent signal have been conserved in the findFIASignal function.

sleep

If not 0 densities are plotted every sleep ms.

dmzGroup

A minimum mz deviation value which can be considered over the deviation in ppm if it is higher. This account for low mass deviation.

fracGroup

The minimum fraction of samples of a class required to make a group.

Value

A proFIAset object with the group slot filled. See proFIAset-class.

Examples

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if(require("plasFIA")){
#proFIAset object is loaded
data(plasSet)

#Parameters are defined.
ppm_group <- 1
dmz_group <- 0.0005
frac_group<-0.2

plasSet<-group.FIA(plasSet,ppmGroup=ppm_group,fracGroup=frac_group,dmzGroup=dmz_group)
plasSet
}

adelabriere/proFIA documentation built on July 12, 2019, 5:46 a.m.