\name{retcor.obiwarp}
\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"),
      col = NULL, ty = NULL, profStep=1,
      center=NULL, 
      response=1, score="cor",
      gapInit=0, gapExtend=0,
      factorDiag=2, factorGap=1,
      localAlignment=0, initPenalty=0) }
}}

\arguments{
  \item{object}{the \code{xcmsSet} object} 
  \item{plottype}{if \code{deviation} plot retention time deviation}
  \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{center}{the index of the sample all others will be aligned
  to. If center==NULL, the sample with the most peaks is chosen as default.}
  \item{response}{Responsiveness of warping.  0 will give a linear warp based
    on start and end points.  100 will use all bijective anchors}

  \item{distFunc}{DistFunc function: cor (Pearson's R) or cor_opt (default,
    calculate only 10\% diagonal band of distance matrix, better
    runtime), cov (covariance), prd (product), euc (Euclidean distance)}
    
  \item{gapInit}{Penalty for Gap opening, see below}
  \item{gapExtend}{Penalty for Gap enlargement, see below}
  \item{factorDiag}{Local weighting applied to diagonal moves in alignment.}
  \item{factorGap}{Local weighting applied to gap moves in alignment.}
  \item{localAlignment}{Local rather than global alignment}
  \item{initPenalty}{Penalty for initiating alignment (for local
  alignment only) Default: 0}

Default gap penalties: (gapInit, gapExtend) [by distFunc type]:
'cor' = '0.3,2.4'
'cov' = '0,11.7'
'prd' = '0,7.8'
'euc' = '0.9,1.8'
}
\value{
  An \code{xcmsSet} object
}
\seealso{
  \code{\link{xcmsSet-class}},
}
\keyword{methods}