\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-class]{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[flowQ]{writeQAReport}}.
}
\usage{
 
 qaProcess.ECDFPlot(flowList, dyes=NULL,outdir="QAReport",
		    alpha=0.05, absolute.value=NULL,sum.dimensions=NULL,
		    det.dimensions=NULL, pdf=TRUE,  
		    name="ECDF",...)
}

\arguments{
  
  \item{flowList}{ A list of \code{\link[flowCore:flowSet-class]{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-class]{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{absolute.value}{If provided, the absolute.value is used for the 
  outlier detection and the alpha argument is ignored. defualt is NULL}
   \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, default is NULL where the dimensions are automatically
  selected.} 
 \item{pdf}{boolen value determinining if pdf files or jpeg images will be 
	    produced by the QA process} 
 \item{name}{The name of the process used for the headings in the HTML
    output.}
  \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[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{ Nishant Gopalakrishnan }


\seealso{
  \code{\link[flowQ]{writeQAReport}},
  \code{\link[flowQ]{qaReport}},
  \code{\link[flowQ:qaProcess-class]{qaProcess}},
  \code{\link[flowQ]{qaProcess.DensityPlot}}
  \code{\link[flowQ]{qaProcess.marginevents}},
  \code{\link[flowQ]{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 }