\name{FAMEoutliers}
\alias{FAMEoutliers}
\title{ FAME outlier detection }
\description{
    A function to detect retention time marker (FAME) outliers.
}
\usage{
FAMEoutliers(samples, RImatrix, pdffile = NA, startDay = NA, endDay = NA,
             threshold = 3, group.threshold = 0.05)
}
\arguments{
  \item{samples}{ A \code{tsSample} object created by \code{ImportSamples} function. }
  \item{RImatrix}{ A retention time matrix of the found retention time markers. }
  \item{pdffile}{ A character string naming a PDF file where the FAMEs report
    will be saved. }
  \item{startDay}{ A numeric vector with the starting days of your day groups. }
  \item{endDay}{ A numeric vector with the ending days of your day groups. }
  \item{threshold}{ A standard deviations cutoff to detect outliers. }
  \item{group.threshold}{ A numeric cutoff to detect day groups based on hierarchical
    clustering. Must be between \code{0..1}.}
}
\details{
    If no \code{pdffile} argument is given, the report will be saved on a file called
    \code{"TargetSearch-YYYY-MM-DD.FAME-report.pdf"}, where \code{YYYY-MM-DD} is a
    date.

    If both \code{startDay} and \code{endDay} are not given, the function will try
    to detect day groups using a hierarchical clustering approach by cutting the tree
    using \code{group.threshold} as cutoff height.

    Retention time markers that deviate more than \code{threshold} standard
    deviations from the    mean of their day group will be identified as outliers.
}
\value{
    A logical matrix of the same size of \code{RImatrix}. A \code{TRUE} value indicates
    that the retention time marker in that particular sample is an outlier.
}
\examples{
require(TargetSearchData)
data(TargetSearchData)

# find the retention marker outliers of the example data and save it in "outlier.pdf"
outliers <- FAMEoutliers(sampleDescription, RImatrix, pdffile = "outlier.pdf")

# find the outliers (although they are reported in the output PDF file)
apply(outliers, 1, which)

}
\author{Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig }
\seealso{ \code{\link{RIcorrect}}, \code{\link{ImportSamples}} }