group.density {xcms} | R Documentation

## Group peaks from different samples together

### Description

Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.

### Arguments

`object` | the `xcmsSet` object
`minfrac` | minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group
`minsamp` | minimum number of samples necessary in at least one of the sample groups for it to be a valid group
`bw` | bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram
`mzwid` | width of overlapping m/z slices to use for creating peak density chromatograms and grouping peaks across samples
`max` | maximum number of groups to identify in a single m/z slice
`sleep` | seconds to pause between plotting successive steps of the peak grouping algorithm. peaks are plotted as points showing relative intensity. identified groups are flanked by dotted vertical lines.

### Value

An `xcmsSet` object with peak group assignments and statistics.

### Methods

object = "xcmsSet"

  `group(object, bw = 30, minfrac = 0.5, minsamp = 1, mzwid = 0.25, max = 50, sleep = 0)`

### See Also

`do_groupChromPeaks_density` for the core API function performing the analysis. `xcmsSet-class`, `density`

[Package xcms version 3.16.1 Index]