group.mzClust {xcms} | R Documentation

## Group Peaks via High Resolution Alignment

### Description

Runs high resolution alignment on single spectra samples stored in a given xcmsSet.

### 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.

### Methods

object = "xcmsSet"

  `group(object, method="mzClust", mzppm = 20, mzabs = 0, minsamp = 1, minfrac=0)`

### 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)

### See Also

`xcmsSet-class`,

### Examples

    ## Not run:
    library(msdata)
    mzdatapath <- system.file("fticr", package = "msdata")
    mzdatafiles <- list.files(mzdatapath, recursive = TRUE, full.names = TRUE)

    xs <- xcmsSet(method="MSW", files=mzdatafiles, scales=c(1,7),
                  SNR.method='data.mean' , winSize.noise=500,
                  peakThr=80000,  amp.Th=0.005)

    xsg <- group(xs, method="mzClust")

    ## End(Not run)

[Package xcms version 3.9.1 Index]