\HeaderA{retcor-methods}{Align retention times across samples with Obiwarp}{retcor.Rdash.methods}
\aliasA{retcor.obiwarp}{retcor-methods}{retcor.obiwarp}
\aliasA{retcor.obiwarp,xcmsSet-method}{retcor-methods}{retcor.obiwarp,xcmsSet.Rdash.method}
\keyword{methods}{retcor-methods}
\begin{Description}\relax
Calculate retention time deviations for each sample.
It is based on the code at \url{http://obi-warp.sourceforge.net/}.
However, this function is able to align multiple samples, by a
center-star strategy. 

For the original publication see

Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by
Ordered Bijective Interpolated Warping John T. Prince and, Edward
M. Marcotte Analytical Chemistry 2006 78 (17), 6140-6152
\end{Description}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] the \code{xcmsSet} object
\item[\code{plottype}] if \code{deviation} plot retention time deviation points and
regression fit, and if \code{mdevden} also plot peak overall
peak density and retention time correction peak density

\item[\code{col}] vector of colors for plotting each sample
\item[\code{ty}] vector of line and point types for plotting each sample
\item[\code{profStep}] step size (in m/z) to use for profile generation from the raw data files
\item[\code{r}] Responsiveness of warping.  0 will give a linear warp based
on start and end points.  100 will use all bijective anchors
\item[\code{g}] Gap penalty given in comma separated string: initiate,extend
(*)Defaults: (gap\_init,gap\_extend) [by score type]:
'cor' = '0.3,2.4'
'cov' = '0,11.7'
'prd' = '0,7.8'
'euc' = '0.9,1.8'
\item[\code{cor}] Score function: (*)cor (Pearson's R) or cor\_opt (better runtime), cov (covariance),
prd (product), euc (Euclidean distance)
\item[\code{l}] Local rather than *global alignment
\item[\code{i\_}] Penalty for initiating alignment (for local alignment only)
(*)Default: 0
\end{ldescription}
\end{Arguments}
\begin{Value}
An \code{xcmsSet} object
\end{Value}
\begin{Section}{Methods}
\describe{
\item[object = "xcmsSet"] retcor(object, method="obiwarp", plottype = c("none", "deviation",
"mdevden"),col = NULL, ty = NULL, profStep=1, r=NULL, g=NULL, cor =
NULL, l=NULL, i\_=0) 
}
\end{Section}
\begin{SeeAlso}\relax
\code{\LinkA{xcmsSet-class}{xcmsSet.Rdash.class}},
\end{SeeAlso}

