xcmsSet-class {xcms}R Documentation

Class xcmsSet, a class for preprocessing peak data

Description

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 from the Class

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", ...).

Slots

peaks:
matrix containing peak data
groups:
matrix containing statistics about peak groups
groupidx:
list containing indices of peaks in each group
sampnames:
character vector with names of each sample
sampclass:
factor containing sample classes
rt:
list containing two lists, raw and corrected, each containing retention times for every scan of every sample
cdfpaths:
character vector with absolute path name of each NetCDF file
profinfo:
list containing two values, method - profile generation method, and step - profile m/z step size

Methods

c
signature("xcmsSet"): combine objects together
cdfpaths<-
signature(object = "xcmsSet"): set cdfpaths slot
cdfpaths
signature(object = "xcmsSet"): get cdfpaths slot
diffreport
signature(object = "xcmsSet"): create report of differentially regulated ions including EICs
fillPeaks
signature(object = "xcmsSet"): fill in peak data for groups with missing peaks
getEIC
signature(object = "xcmsSet"): get list of EICs for each sample in the set
groupidx<-
signature(object = "xcmsSet"): set groupidx slot
groupidx
signature(object = "xcmsSet"): get groupidx slot
groupnames
signature(object = "xcmsSet"): get textual names for peak groups
groups<-
signature(object = "xcmsSet"): set groups slot
groups
signature(object = "xcmsSet"): get groups slot
groupval
signature(object = "xcmsSet"): get matrix of values from peak data with a row for each peak group
group
signature(object = "xcmsSet"): find groups of peaks across samples that share similar m/z and retention times
peaks<-
signature(object = "xcmsSet"): set peaks slot
peaks
signature(object = "xcmsSet"): get peaks slot
plotrt
signature(object = "xcmsSet"): plot retention time deviation profiles
profinfo<-
signature(object = "xcmsSet"): set profinfo slot
profinfo
signature(object = "xcmsSet"): get profinfo slot
retcor
signature(object = "xcmsSet"): use initial grouping of peaks to do nonlinear loess retention time correction
sampclass<-
signature(object = "xcmsSet"): set sampclass slot
sampclass
signature(object = "xcmsSet"): get sampclass slot
sampnames<-
signature(object = "xcmsSet"): set sampnames slot
sampnames
signature(object = "xcmsSet"): get sampnames slot
split
signature("xcmsSet"): divide into a list of objects

Note

No notes yet.

Author(s)

Colin A. Smith, csmith@scripps.edu

References

A parallel effort in metabolite profiling data sharing: http://metlin.scripps.edu/

See Also

xcmsSet


[Package xcms version 1.4.0 Index]