groupFWHM {CAMERA} | R Documentation |
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.
groupFWHM(object, sigma = 6 , perfwhm = 0.6, intval = "maxo")
object |
the |
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 |
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.
Carsten Kuhl <ckuhl@ipb-halle.de>
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)