groupDen {CAMERA} | R Documentation |
Group peaks of a xsAnnotate object according to peak distributions in chromatographic time into pseudospectra-groups. Works analogous as the group.density method of xcms. Returns xsAnnotate object with pseudospectra informations.
groupDen(object, bw = 5 , ...)
object |
the |
bw |
bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram |
... |
Further Arguments, NYI |
The grouping strongly depends on the bw parameter. For an UPLC a good starting point is smaller or around 1.
Returns a grouped xsAnnotate object.
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)) xsa <- xsAnnotate(xs) xsa.grp <- groupDen(xsa, bw=0.5) #Multiple sample library(faahKO) xs <- group(faahko) #With specific selected sample xsa <- xsAnnotate(xs, sample=1) xsa.grp <- groupDen(xsa) #With automatic selection xsa.auto <- xsAnnotate(xs) xsa.grp.auto <- groupDen(xsa.auto)