GroupPeakList: Group peak list

In xia-lab/MetaboAnalystR: An R Package for Comprehensive Analysis of Metabolomics Data

Group peak list

Description

Group peaks from the peak list based on position using the XCMS grouping algorithm (align peaks wrt, rt, and mz). For NMR peaks, need to change ppm -> mz and add dummy rt. If the data is 2-column MS, first need to add dummy rt. If the data is 3-column MS, the data can be used directly. The default mzwid for MS is 0.25 m/z, and for NMR is 0.03 ppm. The default bw is 30 for LCMS, and 5 for GCMS.

Usage

GroupPeakList(mSetObj=NA, mzwid, bw, minfrac, minsamp, max)

Arguments

mSetObj	Input the name of the created mSetObj (see InitDataObjects)
mzwid	define the width of overlapping m/z slices to use for creating peak density chromatograms and grouping peaks across samples
bw	define the bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram
minfrac	define the minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group
minsamp	define the minimum number of samples necessary in at least one of the sample groups for it to be a valid group
max	define the maximum number of groups to identify in a single m/z slice

Author(s)

Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MetaboAnalystR documentation built on April 5, 2025, 11:15 p.m.