\HeaderA{collect-methods}{Collect MS$\textasciicircum{}n$ peaks into xcmsFragments}{collect.Rdash.methods}
\aliasA{collect}{collect-methods}{collect}
\aliasA{collect,xcmsFragments-method}{collect-methods}{collect,xcmsFragments.Rdash.method}
\aliasA{collect,xcmsRaw-method}{collect-methods}{collect,xcmsRaw.Rdash.method}
\keyword{methods}{collect-methods}
\begin{Description}\relax
Collecting Peaks into \code{\LinkA{xcmsFragments}{xcmsFragments.Rdash.class}}s from several
MS-runs using \code{\LinkA{xcmsSet}{xcmsSet.Rdash.class}} and
\code{\LinkA{xcmsRaw}{xcmsRaw.Rdash.class}}.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] (empty) \code{\LinkA{xcmsFragments-class}{xcmsFragments.Rdash.class}} object
\item[\code{xs}] A \code{\LinkA{xcmsSet-class}{xcmsSet.Rdash.class}} object which contains
picked ms1-peaks from several experiments
\item[\code{compMethod}] ("floor", "round", "none"): compare-method which is
used to find the parentpeak of a MSnpeak through comparing the
MZ-values of the  MS1peaks with the MSnParentPeaks.
\item[\code{snthresh, mzgap, uniq}] these are the paramters for the
getspec-peakpicker included in xcmsRaw.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
After running collect(xFragments,xSet) The peaktable of the
xcmsFragments includes the ms1Peaks from all experinemts stored in a
xcmsSet-object. Further it contains the relevant msN-peaks from the
xcmsRaw-objects, which were created temporarily with the paths in
xcmsSet.
\end{Details}
\begin{Value}
A matrix with columns:
\begin{ldescription}
\item[\code{peakID}] unique identifier of every peak

\item[\code{MSnParentPeakID}] PeakID of the parentpeak of a msLevel\textgreater{}1 - peak, it is 0 if the peak is msLevel 1.

\item[\code{msLevel}] The msLevel of the peak.

\item[\code{rt}] retention time of the peak midpoint

\item[\code{mz}] the mz-Value of the peak

\item[\code{intensity}] the intensity of the peak

\item[\code{sample}] the number of the sample from the xcmsSet

\end{ldescription}
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsFragments"] \code{
    collect(object, ...)
   }

}
\end{Section}

