MS Data

Description Usage Arguments Details Value Author(s) See Also Examples

Reads the raw data using xcms, group each extracted ion according to their retention time using CAMERA and attaches them to an already created peaksDataset object

1	addXCMSPeaks(files, object, peakPicking=c('cwt','mF'), ...)

`files`	character vector of same length as `object@rawdata` (user ensures the order matches)
`object`	a `peaksDataset` object.
`peakPicking`	Methods to use for peak detection. See details.
`...`	arguments passed on to `xcmsSet` and `annotate`

Repeated calls to xcmsSet and annotate to perform peak-picking and deconvolution. The peak detection results are added to the original peaksDataset object. Two peak detection alorithms are available: continuous wavelet transform (peakPicking=c('cwt')) and the matched filter approach (peakPicking=c('mF')) described by Smith et al (2006). For further information consult the xcms package manual.

peaksDataset object

Riccardo Romoli riccardo.romoli@unifi.it

peaksDataset findPeaks.matchedFilter findPeaks.centWave xcmsRaw-class

# need access to CDF (raw data)
require(gcspikelite)
gcmsPath <- paste(find.package("gcspikelite"), "data", sep="/")

# full paths to file names
cdfFiles <- dir(gcmsPath, "CDF", full=TRUE)

# create a 'peaksDataset' object and add XCMS peaks to it
pd <- peaksDataset(cdfFiles[1], mz=seq(50,550), rtrange=c(7.5,8.5))
pd <- addXCMSPeaks(cdfFiles[1], pd, peakPicking=c('mF'),
                   snthresh=3, fwhm=4, step=1, steps=2, mzdiff=0.5)