\name{qaProcess.ECDFPlot}
\alias{qaProcess.ECDFPlot}

\title{  Creates a QA process for comparisons of ECDF's across multiple samples }
\description{
   This function takes a list of \code{\link[flowCore]{flowSet}} as input and
  creates all necessary outputs for an 'ecdfOutliers' type of QA
  process. Objects created by this function can be laid out as HTML
  using \code{\link{writeQAReport}}.
}
\usage{
 
 qaProcess.ECDFPlot(flowList,dyes=NULL,outdir="QAReport",
			alpha=0.05,det.dimensions=c(400,400),pdf=FALSE,...)
}

\arguments{
  
  \item{flowList}{ A list of \code{\link[flowCore]{flowSet}} }
  \item{dyes}{Flow parameters to be compared across multiple samples. 
   If set to NULL, all parameters that are duplicated across the list of 
    \code{\link[flowCore]{flowSet}} are identified and compared.}
 \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 every time. }
 \item{alpha}{Outlier mislabeling rate}
 \item{det.dimensions}{the dimensions of each image generated by the QA process.}
 \item{pdf}{boolen value determinining if pdf files or jpeg images will be 
	    produced by the QA process} 
  \item{...}{Further arguments.}

 }
 \details{
   
  QA processes of type 'ECDFPLot' detects differences in the empirical cumulative
  distribution of  flow parameters across multiple 
  samples.A summary measure based on the sum of the pairwise KL
  Distances of ECDF plots across multiple samples is used as a parameter to 
 flag patient panels that are potential outliers.
  
  For more details on how to layout \code{\link{qaProcess}} objects to
  HTML, see \code{\link{writeQAReport}} and \code{\link{qaReport}}.
  
}
\value{
  
  An object of class \code{\link{qaProcess}}.
  
}

\author{ Nishant Gopalakrishnan }


\seealso{
  \code{\link{writeQAReport}}, \code{\link{qaReport}},
  \code{\link{qaProcess}}, \code{\link{qaProcess.marginevents}},
  \code{\link{qaProcess.DensityPlot}}, \code{\link{qaProcess.2DStatsPlot}}

}


\examples{
data(qData)
dyes<- c("FSC-A","SSC-A")
dest <- tempdir()
resFSCECDF <- qaProcess.ECDFPlot(qData,dyes=dyes,outdir=dest,alpha=0.4,pdf=TRUE)
resFSCECDF
%writeQAReport(nData[[1]], list(resFSCECDF), outdir=dest,pdf=TRUE)

}

\keyword{ dynamic }