group.density: Group peaks from different samples together

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

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

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.