\name{retcor-methods}
\docType{methods}
\alias{retcor.obiwarp}
\alias{retcor.obiwarp,xcmsSet-method}

\title{Align retention times across samples with Obiwarp}

\description{
  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
}

\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) }
}}

\arguments{
  \item{object}{the \code{xcmsSet} object} 
  \item{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{col}{vector of colors for plotting each sample}
  \item{ty}{vector of line and point types for plotting each sample}
  \item{profStep}{step size (in m/z) to use for profile generation from the raw data files}

\item{r}{Responsiveness of warping.  0 will give a linear warp based
	    on start and end points.  100 will use all bijective anchors}
\item{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{cor}{Score function: (*)cor (Pearson's R) or cor\_opt (better runtime), cov (covariance),
                   prd (product), euc (Euclidean distance)}
\item{l}{Local rather than *global alignment}
\item{i\_}{Penalty for initiating alignment (for local alignment only)
                   (*)Default: 0}
}
\value{
  An \code{xcmsSet} object
}
\seealso{
  \code{\link{xcmsSet-class}},
}
\keyword{methods}