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

In sneumann/CAMERA: Collection of annotation related methods for mass spectrometry data

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 <[e-mail]>

Examples

 library(CAMERA)
 #Single sample 
 file <- system.file('mzML/MM14.mzML', 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)

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