Group Peaks via High Resolution Alignment

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

Value

Returns a xcmsSet with slots groups and groupindex set.

See also

xcmsSet-class,

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) { # \dontrun{
library(MsDataHub)
mzMLfiles <- c(MsDataHub::HAM004_641fE_14.11.07..Exp1.extracted.mzML(),
               MsDataHub::HAM004_641fE_14.11.07..Exp2.extracted.mzML(),
               MsDataHub::HAM005_641fE_14.11.07..Exp1.extracted.mzML(),
               MsDataHub::HAM005_641fE_14.11.07..Exp2.extracted.mzML())

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")
} # }