CAMERA (version 1.28.0)

groupDen: Density-Grouping of LC/ESI-MS data

Description

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.

Usage

groupDen(object, bw = 5 , ...)

Arguments

object

the xsAnnotate object

bw

bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram

...

Further Arguments, NYI

Value

Returns a grouped xsAnnotate object.

Details

The grouping strongly depends on the bw parameter. For an UPLC a good starting point is smaller or around 1.

Examples

 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)