\HeaderA{retcor-methods}{Correct retention time from different samples}{retcor.Rdash.methods}
\aliasA{retcor}{retcor-methods}{retcor}
\aliasA{retcor,xcmsSet-method}{retcor-methods}{retcor,xcmsSet.Rdash.method}
\keyword{methods}{retcor-methods}
\begin{Description}\relax
To correct differences between retention times between different
samples, a number of of methods exist in XCMS. \code{retcor}
is the generic method.
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] \code{\LinkA{xcmsSet-class}{xcmsSet.Rdash.class}} object
\item[\code{method}] Method to use for retention time correction. See details.
\item[\code{...}] Optional arguments to be passed along
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Different algorithms can be used by specifying them with the
\code{method} argument. For example to use the approach described by
Smith et al (2006) one would use: \code{retcor(object,
  method="loess")}. This is also the default.

Further arguments given by \code{...} are
passed through to the function implementing
the \code{method}. 

A character vector of \emph{nicknames} for the 
algorithms available is returned by 
\code{getOption("BioC")\$xcms\$retcor.methods}.
If the nickname of a method is called "loess",
the help page for that specific method can
be accessed with \code{?retcor.loess}.
\end{Details}
\begin{Value}
An \code{xcmsSet} object with corrected retntion times.
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsSet"] \code{
    retcor(object, ...)
  }

}
\end{Section}
\begin{SeeAlso}\relax
\code{\LinkA{retcor.loess}{retcor.loess}}
\code{\LinkA{retcor.obiwarp}{retcor.obiwarp}}
\code{\LinkA{xcmsSet-class}{xcmsSet.Rdash.class}},
\end{SeeAlso}

