groupFWHM {CAMERA} | R Documentation

## FWHM-Grouping of LC/ESI-MS data

### Description

Group peaks of a xsAnnotate object according to there retention time into pseudospectra-groups. Uses the peak FWHMs as grouping borders. Returns xsAnnotate object with pseudospectra informations.

### Usage

      groupFWHM(object, sigma = 6 , perfwhm = 0.6, intval = "maxo")

### Arguments

`object` | the `xsAnnotate` object
`sigma` | the multiplier of the standard deviation
`perfwhm` | percentage of the width of the FWHM
`intval` | intensity values for ordering. Allowed values are into, maxo, intb

### Details

Every peak who eluate at the same time-point as a selected peak, will be part of the group. Same time-point is defined about the Rt_med +/- FWHM * perfwhm. For a single sample `xcmsSet` the selection of peaks starts at the most abundant and goes down to the smaller ones. With a multiple sample set the automatic selection uses the most abundant peak as an representative for every feature group, according to the xcms grouping. With the xsAnnotate sample parameter a sample selection can be defined to use only specific samples. See `xsAnnotate-class` for further information. The FWHM (full width at half maximum) of a peak is estimated as FWHM = SD * 2.35. For the calculation of the SD, the peak is assumed as normal distributed.

### Author(s)

Carsten Kuhl <ckuhl@ipb-halle.de>

### Examples

     library(CAMERA)
     #Single sample
     file <- system.file('mzdata/MM14.mzdata', package = "CAMERA")
     xs   <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5,10))
     an   <- xsAnnotate(xs)
     an   <- groupFWHM(an)

     #Multiple sample
     library(faahKO)
     xs   <- group(faahko)

     #With specific selected sample
     xs.anno  <- xsAnnotate(xs, sample=1)
     xs.group <- groupFWHM(xs.anno)

     #With automatic selection
     xs.anno.auto  <- xsAnnotate(xs)
     xs.group.auto <- groupFWHM(xs.anno.auto)

[Package CAMERA version 1.48.0 Index]