| xcmsSet-class {xcms} | R Documentation |
This class transforms a set of peaks from multiple LC/MS or GC/MS samples into a matrix of preprocessed data. It groups the peaks and does nonlinear retention time correction without internal standards. It fills in missing peak values from raw data. Lastly, it generates extracted ion chromatograms for ions of interest.
Objects can be created with the xcmsSet constructor
which gathers peaks from a set NetCDF files. Objects can also be
created by calls of the form new("xcmsSet", ...).
peaks:groups:groupidx:sampnames:sampclass:rt:raw and corrected,
each containing retention times for every scan of every sample
cdfpaths:profinfo:method - profile generation
method, and step - profile m/z step size
signature("xcmsSet"): combine objects together
signature(object = "xcmsSet"): set cdfpaths slot
signature(object = "xcmsSet"): get cdfpaths slot
signature(object = "xcmsSet"): create report of
differentially regulated ions including EICs
signature(object = "xcmsSet"): fill in peak data for
groups with missing peaks
signature(object = "xcmsSet"): get list of EICs for
each sample in the set
signature(object = "xcmsSet"): set groupidx slot
signature(object = "xcmsSet"): get groupidx slot
signature(object = "xcmsSet"): get textual names for
peak groups
signature(object = "xcmsSet"): set groups slot
signature(object = "xcmsSet"): get groups slot
signature(object = "xcmsSet"): get matrix of values
from peak data with a row for each peak group
signature(object = "xcmsSet"): find groups of peaks
across samples that share similar m/z and retention times
signature(object = "xcmsSet"): set peaks slot
signature(object = "xcmsSet"): get peaks slot
signature(object = "xcmsSet"): plot retention time
deviation profiles
signature(object = "xcmsSet"): set profinfo slot
signature(object = "xcmsSet"): get profinfo slot
signature(object = "xcmsSet"): use initial grouping
of peaks to do nonlinear loess retention time correction
signature(object = "xcmsSet"): set sampclass slot
signature(object = "xcmsSet"): get sampclass slot
signature(object = "xcmsSet"): set sampnames slot
signature(object = "xcmsSet"): get sampnames slot
signature("xcmsSet"): divide into a list of objects
No notes yet.
Colin A. Smith, csmith@scripps.edu
A parallel effort in metabolite profiling data sharing: http://metlin.scripps.edu/