groupFWHM-methods: FWHM-Grouping of LC/ESI-MS data

groupFWHMR Documentation

FWHM-Grouping of LC/ESI-MS data


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


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



the xsAnnotate object


the multiplier of the standard deviation


percentage of the width of the FWHM


intensity values for ordering. Allowed values are into, maxo, intb


Every peak that shares a retention time with 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 least abundant. 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.


Carsten Kuhl <>


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

 #Multiple sample 
 xs   <- group(faahko)

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

sneumann/CAMERA documentation built on April 5, 2024, 2:33 a.m.