\HeaderA{xcmsSet-class}{Class xcmsSet, a class for preprocessing peak data}{xcmsSet.Rdash.class}
\aliasA{cdfpaths}{xcmsSet-class}{cdfpaths}
\aliasA{cdfpaths,xcmsSet-method}{xcmsSet-class}{cdfpaths,xcmsSet.Rdash.method}
\aliasA{cdfpaths<\Rdash}{xcmsSet-class}{cdfpaths<.Rdash.}
\aliasA{cdfpaths<-,xcmsSet-method}{xcmsSet-class}{cdfpaths<.Rdash.,xcmsSet.Rdash.method}
\aliasA{groupidx}{xcmsSet-class}{groupidx}
\aliasA{groupidx,xcmsSet-method}{xcmsSet-class}{groupidx,xcmsSet.Rdash.method}
\aliasA{groupidx<\Rdash}{xcmsSet-class}{groupidx<.Rdash.}
\aliasA{groupidx<-,xcmsSet-method}{xcmsSet-class}{groupidx<.Rdash.,xcmsSet.Rdash.method}
\aliasA{groups}{xcmsSet-class}{groups}
\aliasA{groups,xcmsSet-method}{xcmsSet-class}{groups,xcmsSet.Rdash.method}
\aliasA{groups<\Rdash}{xcmsSet-class}{groups<.Rdash.}
\aliasA{groups<-,xcmsSet-method}{xcmsSet-class}{groups<.Rdash.,xcmsSet.Rdash.method}
\aliasA{peaks}{xcmsSet-class}{peaks}
\aliasA{peaks,xcmsSet-method}{xcmsSet-class}{peaks,xcmsSet.Rdash.method}
\aliasA{peaks<\Rdash}{xcmsSet-class}{peaks<.Rdash.}
\aliasA{peaks<-,xcmsSet-method}{xcmsSet-class}{peaks<.Rdash.,xcmsSet.Rdash.method}
\aliasA{profinfo}{xcmsSet-class}{profinfo}
\aliasA{profinfo,xcmsSet-method}{xcmsSet-class}{profinfo,xcmsSet.Rdash.method}
\aliasA{profinfo<\Rdash}{xcmsSet-class}{profinfo<.Rdash.}
\aliasA{profinfo<-,xcmsSet-method}{xcmsSet-class}{profinfo<.Rdash.,xcmsSet.Rdash.method}
\aliasA{sampclass}{xcmsSet-class}{sampclass}
\aliasA{sampclass,xcmsSet-method}{xcmsSet-class}{sampclass,xcmsSet.Rdash.method}
\aliasA{sampclass<\Rdash}{xcmsSet-class}{sampclass<.Rdash.}
\aliasA{sampclass<-,xcmsSet-method}{xcmsSet-class}{sampclass<.Rdash.,xcmsSet.Rdash.method}
\aliasA{sampnames<\Rdash}{xcmsSet-class}{sampnames<.Rdash.}
\aliasA{sampnames<-,xcmsSet-method}{xcmsSet-class}{sampnames<.Rdash.,xcmsSet.Rdash.method}
\aliasA{show,xcmsSet-method}{xcmsSet-class}{show,xcmsSet.Rdash.method}
\keyword{classes}{xcmsSet-class}
\begin{Description}\relax
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.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created with the \code{\LinkA{xcmsSet}{xcmsSet}} constructor
which gathers peaks from a set NetCDF files. Objects can also be
created by calls of the form \code{new("xcmsSet", ...)}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{peaks}:] matrix containing peak data

\item[\code{groups}:] matrix containing statistics about peak groups

\item[\code{groupidx}:] list containing indices of peaks in each group

\item[\code{sampnames}:] character vector with names of each sample

\item[\code{sampclass}:] factor containing sample classes

\item[\code{rt}:] list containing two lists, \code{raw} and \code{corrected},
each containing retention times for every scan of every sample

\item[\code{cdfpaths}:] character vector with absolute path name of each NetCDF file

\item[\code{profinfo}:] list containing two values, \code{method} - profile generation
method, and \code{step} - profile m/z step size

}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[\LinkA{c}{c}] \code{signature("xcmsSet")}: combine objects together

\item[cdfpaths<-] \code{signature(object = "xcmsSet")}: set \code{cdfpaths} slot

\item[cdfpaths] \code{signature(object = "xcmsSet")}: get \code{cdfpaths} slot

\item[\LinkA{diffreport}{diffreport}] \code{signature(object = "xcmsSet")}: create report of
differentially regulated ions including EICs

\item[\LinkA{fillPeaks}{fillPeaks}] \code{signature(object = "xcmsSet")}: fill in peak data for
groups with missing peaks

\item[\LinkA{getEIC}{getEIC}] \code{signature(object = "xcmsSet")}: get list of EICs for
each sample in the set

\item[groupidx<-] \code{signature(object = "xcmsSet")}: set \code{groupidx} slot

\item[groupidx] \code{signature(object = "xcmsSet")}: get \code{groupidx} slot

\item[\LinkA{groupnames}{groupnames}] \code{signature(object = "xcmsSet")}: get textual names for
peak groups

\item[groups<-] \code{signature(object = "xcmsSet")}: set \code{groups} slot

\item[groups] \code{signature(object = "xcmsSet")}: get \code{groups} slot

\item[\LinkA{groupval}{groupval}] \code{signature(object = "xcmsSet")}: get matrix of values
from peak data with a row for each peak group

\item[\LinkA{group}{group}] \code{signature(object = "xcmsSet")}: find groups of peaks
across samples that share similar m/z and retention times

\item[peaks<-] \code{signature(object = "xcmsSet")}: set \code{peaks} slot

\item[peaks] \code{signature(object = "xcmsSet")}: get \code{peaks} slot

\item[\LinkA{plotrt}{plotrt}] \code{signature(object = "xcmsSet")}: plot retention time
deviation profiles

\item[profinfo<-] \code{signature(object = "xcmsSet")}: set \code{profinfo} slot

\item[profinfo] \code{signature(object = "xcmsSet")}: get \code{profinfo} slot

\item[\LinkA{retcor}{retcor}] \code{signature(object = "xcmsSet")}: use initial grouping
of peaks to do nonlinear loess retention time correction

\item[sampclass<-] \code{signature(object = "xcmsSet")}: set \code{sampclass} slot

\item[sampclass] \code{signature(object = "xcmsSet")}: get \code{sampclass} slot

\item[sampnames<-] \code{signature(object = "xcmsSet")}: set \code{sampnames} slot

\item[\LinkA{sampnames}{sampnames}] \code{signature(object = "xcmsSet")}: get \code{sampnames} slot

\item[\LinkA{split}{split}] \code{signature("xcmsSet")}: divide into a list of objects

}
\end{Section}
\begin{Note}\relax
No notes yet.
\end{Note}
\begin{Author}\relax
Colin A. Smith, \email{csmith@scripps.edu}
\end{Author}
\begin{References}\relax
A parallel effort in metabolite profiling data sharing:
\url{http://metlin.scripps.edu/}
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{xcmsSet}{xcmsSet}}
\end{SeeAlso}

