CAMERA (version 1.28.0)

groupFWHM: 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.

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)