group.density: Group peaks from different samples together

Description Arguments Value Methods See Also

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


xcms documentation built on May 18, 2019, 2 a.m.