\HeaderA{getEIC-methods}{Get extracted ion chromatograms for specified m/z ranges}{getEIC.Rdash.methods}
\aliasA{getEIC}{getEIC-methods}{getEIC}
\aliasA{getEIC,xcmsRaw-method}{getEIC-methods}{getEIC,xcmsRaw.Rdash.method}
\aliasA{getEIC,xcmsSet-method}{getEIC-methods}{getEIC,xcmsSet.Rdash.method}
\keyword{methods}{getEIC-methods}
\keyword{file}{getEIC-methods}
\begin{Description}\relax
Generate multiple extracted ion chromatograms for m/z values of
interest.  For \code{xcmsSet} objects, reread original raw data
and apply precomputed retention time correction, if applicable.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] the \code{xcmsRaw} or \code{xcmsSet} object
\item[\code{mzrange}] either a two column matrix with minimum or maximum m/z or a
matrix of any dimensions containing columns \code{mzmin} and
\code{mzmax}

for \code{xcmsSet} objects, if left blank the group data will
be used instead

\item[\code{rtrange}] a two column matrix the same size as \code{mzrange} with minimum
and maximum retention times between which to return EIC data
points

for \code{xcmsSet} objects, it may also be a single number
specifying the time window around the peak to return EIC data
points

\item[\code{step}] step size to use for profile generation
\item[\code{groupidx}] either character vector with names or integer vector with
indicies of peak groups for which to get EICs

\item[\code{sampleidx}] either character vector with names or integer vector with
indicies of samples for which to get EICs

\item[\code{rt}] \code{"corrected"} for using corrected retention times, or
\code{"raw"} for using raw retention times

\end{ldescription}
\end{Arguments}
\begin{Value}
For \code{xcmsRaw} objects, if \code{rtrange} is NULL, a matrix
with a column for each \code{mzmin}, \code{mzmax} pair. Rows
correspond to individual scans. Otherwise, a list of two column
(retention time/intensity) matricies, one for each \code{mzmin},
\code{mzmax} pair.

For \code{xcmsSet} objects, an \code{xcmsEIC} object.
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsRaw"] \code{getEIC(object, mzrange, rtrange = NULL, step = 0.1)}

\item[object = "xcmsSet"] \code{getEIC(object, mzrange, rtrange = 200, groupidx, 
               sampleidx = sampnames(object), rt = c("corrected", "raw"))}

}
\end{Section}
\begin{SeeAlso}\relax
\code{\LinkA{xcmsRaw-class}{xcmsRaw.Rdash.class}},
\code{\LinkA{xcmsSet-class}{xcmsSet.Rdash.class}},
\code{\LinkA{xcmsEIC-class}{xcmsEIC.Rdash.class}}
\end{SeeAlso}

