addXCMSPeaks: addXCMSPeaks

In rromoli/flagme: Analysis of Metabolomics GC/MS Data

addXCMSPeaks

Description

Add xcms/CAMERA peak detection results

Usage

addXCMSPeaks(
  files,
  object,
  settings = list(),
  minintens = 100,
  minfeat = 6,
  BPPARAM = bpparam(),
  multipleMF = FALSE,
  multipleMFParam = list(fwhm = c(5, 10, 15), mz.abs = 0.2, rt.abs = 2)
)

Arguments

files	list of chromatogram files
object	a peakDataset object
settings	see findPeaks-matchedFilter findPeaks-centWave
minintens	minimum ion intensity to be included into a pseudospectra
minfeat	minimum number of ion to be created a pseudospectra
BPPARAM	a parameter class specifying if and how parallel processing should be performed
multipleMF	logical Try to remove redundant peaks, in this case where there are any peaks within an absolute m/z value of 0.2 and within 3 s for any one sample in the xcmsSet (the largest peak is kept)
multipleMFParam	list. It conteins the settings for the peak-picking. mz_abs represent the the mz range; rt_abs represent thert range
mz.abs	mz range
rt.abs	rt range

Details

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

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.

Value

peaksDataset object

Author(s)

Riccardo Romoli [e-mail]

See Also

peaksDataset findPeaks-matchedFilter findPeaks-centWave xcmsRaw-class

Examples

files <- list.files(path = paste(find.package("gcspikelite"), "data",
                    sep = "/"),"CDF", full = TRUE)
data <- peaksDataset(files[1:2], mz = seq(50, 550), rtrange = c(7.5, 8.5))
## create settings object
mfp <- xcms::MatchedFilterParam(fwhm = 10, snthresh = 5)
cwt <- xcms::CentWaveParam()
data <- addXCMSPeaks(files[1:2], data, settings = mfp, multipleMF = FALSE)
data

rromoli/flagme documentation built on Feb. 10, 2023, 12:59 a.m.