groupDen {CAMERA} | R Documentation

## 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

### Details

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

### Value

Returns a grouped xsAnnotate object.

### Author(s)

Carsten Kuhl <ckuhl@ipb-halle.de>

### 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)

[Package CAMERA version 1.40.0 Index]