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fillPeaks.chrom-methods.Rd
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fillPeaks.chrom-methods.Rd
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\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, nSlaves=0,expand.mz=1,expand.rt=1,min.width.mz=0,min.width.rt=0)}
}
}}
\arguments{
\item{object}{the \code{xcmsSet} object}
\item{nSlaves}{number of slaves/cores to be used for parallel peak filling.
MPI is used if installed, otherwise the snow package is employed for multicore support.}
\item{expand.mz}{Expansion factor for the m/z range used for integration.}
\item{expand.rt}{Expansion factor for the retention time range used for integration.}
\item{min.width.mz}{Minimum m/z range used for integration.}
\item{min.width.rt}{Minimum retention time range used for integration.}
}
\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 (into and maxo).
}
\seealso{
\code{\link{xcmsSet-class}},
\code{\link{getPeaks}}
\code{\link{fillPeaks}}
}
\keyword{methods}
\keyword{file}