groupFWHM-methods: FWHM-Grouping of LC/ESI-MS data

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

FWHM-Grouping of LC/ESI-MS data

Description

Group peaks of a xsAnnotate object according to their retention time into pseudospectra-groups. Uses the peak FWHMs as grouping borders. Returns xsAnnotate object with pseudospectra informations.

Usage

  groupFWHM(object, sigma = 6 , perfwhm = 0.6, intval = "maxo")

Arguments

object	the xsAnnotate object
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

Details

Every peak that shares a retention time with 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 least abundant. 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.

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))
 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)

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