\name{fillPeaks.chrom-methods}
\docType{methods}
%\alias{fillPeaks.chrom-methods}
\alias{fillPeaks.chrom}
\alias{fillPeaks.chrom,xcmsSet-method}
\title{Integrate areas of missing peaks}
\description{
  For each sample, identify peak groups where that sample is not
  represented. For each of those peak groups, integrate the signal
  in the region of that peak group and create a new peak.
}
\section{Methods}{
\describe{
\item{object = "xcmsSet"}{
  \code{fillPeaks.chrom(object)}
}
}}

\arguments{
  \item{object}{the \code{xcmsSet} object}
}
\details{
  After peak grouping, there will always be peak groups that do not
  include peaks from every sample. This method produces intensity
  values for those missing samples by integrating raw data in peak
  group region. In a given group, the start and ending retention
  time points for integration are defined by the median start and
  end points of the other detected peaks. The start and end m/z
  values are similarly determined. Intensities
  can be still be zero, which is a rather unusual intensity for a peak.
  This is the case if e.g. the raw data was threshholded, and the
  integration area contains no actual raw intensities, or if one sample
  is miscalibrated, such thet the raw data points are (just) outside
  the integration area.
  
  Importantly, if retention time correction data is available, the
  alignment information is used to more precisely integrate the
  propper region of the raw data. If the corrected retention time
  is beyond the end of the raw data, the value will be not-a-number (NaN).
  
}
\value{
  A \code{xcmsSet} objects with filled in peak groups.
}

\seealso{
  \code{\link{xcmsSet-class}},
  \code{\link{getPeaks}}
  \code{\link{fillPeaks}}
}
\keyword{methods}
\keyword{file}