\HeaderA{xcmsRaw-class}{Class xcmsRaw, a class for handling raw data}{xcmsRaw.Rdash.class}
\aliasA{profMz}{xcmsRaw-class}{profMz}
\aliasA{profMz,xcmsRaw-method}{xcmsRaw-class}{profMz,xcmsRaw.Rdash.method}
\aliasA{revMz}{xcmsRaw-class}{revMz}
\aliasA{revMz,xcmsRaw-method}{xcmsRaw-class}{revMz,xcmsRaw.Rdash.method}
\aliasA{show,xcmsRaw-method}{xcmsRaw-class}{show,xcmsRaw.Rdash.method}
\aliasA{sortMz}{xcmsRaw-class}{sortMz}
\aliasA{sortMz,xcmsRaw-method}{xcmsRaw-class}{sortMz,xcmsRaw.Rdash.method}
\keyword{classes}{xcmsRaw-class}
\begin{Description}\relax
This class handles processing and visualization of the raw data
from a single LC/MS or GS/MS run. It includes methods for producing
a standard suite of plots including individual spectra, multi-scan
average spectra, TIC, and EIC. It will also produce a feature
list of significant peaks using matched filtration.
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created with the \code{\LinkA{xcmsRaw}{xcmsRaw}} constructor
which reads data from a NetCDF file into a new object.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{env}:] environment with three variables: \code{mz} - concatenated
m/z values for all scans, \code{intensity} - corresponding
signal intensity for each m/z value, and \code{profile} -
matrix represention of the intensity values with columns
representing scans and rows representing equally spaced m/z
values

\item[\code{tic}:] numeric vector with total ion count (intensity) for each scan

\item[\code{scantime}:] numeric vector with acquisition time (in seconds) for each
scan

\item[\code{scanindex}:] integer vector with starting positions of each scan in the
\code{mz} and \code{intensity} variables (note that index
values are based off a 0 initial position instead of 1)

\item[\code{profmethod}:] characer value with name of method used for generating the
profile matrix

\item[\code{mzrange}:] numeric vector of length 2 with minimum and maximum m/z values
represented in the profile matrix

\item[\code{gradient}:] matrix with first row, \code{time}, containing the time point
for interpolation and successive columns representing solvent
fractions at each point

\item[\code{msmsinfo}:] matrix with first row, \code{parent}, containing parent ion
m/z and sucessive columns representing additional information
about fragmentation (energy, etc.)

}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[\LinkA{findPeaks}{findPeaks}] \code{signature(object = "xcmsRaw")}: feature detection using
matched filtration in the chromatographic time domain

\item[\LinkA{getEIC}{getEIC}] \code{signature(object = "xcmsRaw")}: get extracted ion
chromatograms in specified m/z ranges

\item[\LinkA{getPeaks}{getPeaks}] \code{signature(object = "xcmsRaw")}: get data for peaks in
specified m/z and time ranges

\item[\LinkA{getScan}{getScan}] \code{signature(object = "xcmsRaw")}: get m/z and intensity
values for a single mass scan

\item[\LinkA{getSpec}{getSpec}] \code{signature(object = "xcmsRaw")}: get average m/z and
intensity values for multiple mass scans

\item[\LinkA{image}{image}] \code{signature(x = "xcmsRaw")}: get data for peaks in
specified m/z and time ranges

\item[\LinkA{plotChrom}{plotChrom}] \code{signature(object = "xcmsRaw")}: plot a chromatogram
from profile data

\item[\LinkA{plotRaw}{plotRaw}] \code{signature(object = "xcmsRaw")}: plot locations of raw
intensity data points

\item[\LinkA{plotScan}{plotScan}] \code{signature(object = "xcmsRaw")}: plot a mass spectrum
of an individual scan from the raw data

\item[\LinkA{plotSpec}{plotSpec}] \code{signature(object = "xcmsRaw")}: plot a mass spectrum
from profile data

\item[\LinkA{plotSurf}{plotSurf}] \code{signature(object = "xcmsRaw")}: experimental method for
plotting 3D surface of profile data with \code{rgl}.

\item[\LinkA{plotTIC}{plotTIC}] \code{signature(object = "xcmsRaw")}: plot total ion count
chromatogram

\item[\LinkA{profMedFilt}{profMedFilt}] \code{signature(object = "xcmsRaw")}: median filter profile
data in time and m/z dimensions

\item[\LinkA{profMethod\textless{}-}{profMethod\textless.Rlbrace..Rrbrace..Rdash.}] \code{signature(object = "xcmsRaw")}: change the method of
generating the \code{profile} matrix

\item[\LinkA{profMethod}{profMethod}] \code{signature(object = "xcmsRaw")}: get the method of
generating the \code{profile} matrix

\item[profMz] \code{signature(object = "xcmsRaw")}: get vector of m/z values
for each row of the \code{profile} matrix

\item[\LinkA{profRange}{profRange}] \code{signature(object = "xcmsRaw")}: interpret flexible ways
of specifying subsets of the \code{profile} matrix

\item[\LinkA{profStep\textless{}-}{profStep\textless.Rlbrace..Rrbrace..Rdash.}] \code{signature(object = "xcmsRaw")}: change the m/z step
used for generating the \code{profile} matrix

\item[\LinkA{profStep}{profStep}] \code{signature(object = "xcmsRaw")}: get the m/z step used
for generating the \code{profile} matrix

\item[revMz] \code{signature(object = "xcmsRaw")}: reverse the order of the
data points for each scan

\item[sortMz] \code{signature(object = "xcmsRaw")}: sort the data points
by increasing m/z for each scan

}
\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{xcmsRaw}{xcmsRaw}}
\end{SeeAlso}

