Group Peaks via High Resolution Alignment
group.mzClust.Rd
Runs high resolution alignment on single spectra samples stored in a given xcmsSet.
Methods
- object = "xcmsSet"
group(object, method="mzClust", mzppm = 20, mzabs = 0, minsamp = 1, minfrac=0)
Arguments
- object
a xcmsSet with peaks
- mzppm
the relative error used for clustering/grouping in ppm (parts per million)
- mzabs
the absolute error used for clustering/grouping
- minsamp
set the minimum number of samples in one bin
- minfrac
set the minimum fraction of each class in one bin
References
Saira A. Kazmi, Samiran Ghosh, Dong-Guk Shin,
Dennis W. Hill and David F. Grant
Alignment of high resolution mass spectra: development of a heuristic
approach for metabolomics.
Metabolomics, Vol. 2, No. 2, 75-83 (2006)
Examples
if (FALSE) {
library(msdata)
mzMLpath <- system.file("fticr-mzML", package = "msdata")
mzMLfiles <- list.files(mzMLpath, recursive = TRUE, full.names = TRUE)
xs <- xcmsSet(method="MSW", files=mzMLfiles, scales=c(1,7),
SNR.method='data.mean' , winSize.noise=500,
peakThr=80000, amp.Th=0.005)
xsg <- group(xs, method="mzClust")
}