\name{qaProcess.marginevents}
\alias{qaProcess.marginevents}

\title{ Create QA process of type 'marginevents' }
\description{
  This function takes a \code{\link[flowCore:flowSet-class]{flowSet}} as
  input and 
  creates all necessary output for a 'marginevents' type QA
  process. Objects created by this function can be laid out as HTML
  using \code{\link[flowQ]{writeQAReport}}.
}
\usage{

qaProcess.marginevents(set, channels=NULL,side ="both", grouping=NULL, 
    outdir, cFactor=2, absolute.value=NULL, name="margin events",
    sum.dimensions=NULL, det.dimensions=c(3,1), pdf=TRUE, \dots)

}

\arguments{
  
  \item{set}{ A \code{\link[flowCore:flowSet-class]{flowSet}}.}
  
  \item{channels}{ A character vector of channel names for which margin
    events are to be recorded. Will use all available channels except
    for the time channel if \code{NULL}. }

  \item{side}{Object of class \code{"character"}. The margin
       on which to evaluate the filter. Either \code{upper} for the
       upper margin or \code{lower} for the lower margin or \code{both}
       for both margins. }

  \item{grouping}{ A character vector defining one of the variables in
    the phenoData of \code{set} used as a grouping variable. If this
    argument is used and if \code{absolute.value} is \code{NULL}, outlier
    detection will be performed within groups rather than across all
    samples.}
  
  \item{outdir}{ The directory to which the graphical output is to be
    saved. If multiple QA processes are to be combined, make sure to use
    the same directory for all of them.}

  \item{cFactor}{ The outlier threshold at which the QA criterion is
    considered to have failed. This is essentially the factor of
    standard deviations away from the average number of cells per sample
    for the respective channel.}

  \item{absolute.value}{ An absolute percentage of margin events below
    which the QA criterion is considered to be failed. If this argument
    is not \code{NULL}, \code{cFactor} is ignored.}

  \item{name}{ The name of the process used for the headings in the HTML
    output.}
	
   \item{sum.dimensions}{The dimensions of summary plot generated in inches, default
 is NULL where the dimensions are automatically selected}
 
 \item{det.dimensions}{the dimensions of each sub image generated by the QA
  process in inches.} 
  
  \item{pdf}{ Logical indicating whether to create vectorized versions
    of images for this quality process. This should be set to
    \code{FALSE} if disk space is critical, since the pdf versions of
    the image consume much more space on the hard drive compared to the
    bitmap version. Setting the argument to \code{FALSE} will also
    speed up the process.}
  
  \item{\dots}{Further arguments.}
  
}
 
\details{
  
  QA processes of type 'marginevents' record the number of events that
  fall on the margins of the measurement range for each
  channel. Unproportionally high numbers of such events can indicate
  problems with the instrument settings or with compensation. These are
  either determined dynamically as outliers from the typical
  distribution of margin event percentages for the whole set, or, if
  \code{absolute.value} is not \code{NULL}, by an absolute cutoff
  value. If there is a natural grouping among the samples, this can be
  specified using the \code{grouping} argument. In this case, the
  outlier detection will be performed within its respective group for a
  particular sample.
  
  For more details on how to layout
  \code{\link[flowQ:qaProcess-class]{qaProcess}} objects to 
  HTML, see \code{\link[flowQ]{writeQAReport}} and
  \code{\link[flowQ]{qaReport}}. 
  
}
\value{
  An object of class \code{\link[flowQ:qaProcess-class]{qaProcess}}.
}

\author{ Florian Hahne }

\seealso{
    \code{\link[flowQ]{writeQAReport}},
  \code{\link[flowQ]{qaReport}},
  \code{\link[flowQ:qaProcess-class]{qaProcess}},
  \code{\link[flowQ]{qaProcess.timeline}},
  \code{\link[flowQ]{qaProcess.timeflow}},
  \code{\link[flowQ]{qaProcess.cellnumber}}

}

 \examples{
\dontrun{
data(GvHD)
dest <- tempdir()
qp <- qaProcess.marginevents(GvHD, channels=c("FSC-H", "SSC-H"),
  outdir=dest)
qp
}

 }

\keyword{ dynamic }