\name{makeRangedDataOutput}
\alias{makeRangedDataOutput}

\title{Create a RangedData object from a PING output}
\description{
Create a list of 'RangedData' objects from a 'ping' object. The resulting RangedData object can then be analyzed with the 'IRanges' packages and/or exported to bed/wig files with the 'rtracklayer' package.
}
\usage{
makeRangedDataOutput(obj, type="fixed", filter=list(delta=c(0,Inf),se=c(0,Inf),sigmaSqF=c(0,Inf),sigmaSqR=c(0,Inf),score=c(0,Inf)),length=100)
}

\arguments{
  \item{obj}{An object of class 'pingList' as returned by 'PING' when running it on the IP/Control data.}
  \item{type}{The type of intervals to be created. The different types are 'bed', 'wig', 'ci' and 'fixed'. See details for more info.}
  \item{filter}{A list of filters to be used before computing the FDR. By default all regions are included, see details for more info on how to specify the filters.}
  \item{length}{The length to be used for the fixed type 'RangedData', see details.}
}
\details{
'bed' will generate intervals from the forward peak max to the reverse peak max. 'wig' will generate a density profile for the forward and reverse reads. 'bed' and 'wig' types should be used to be exported to wig/bed files to be used with the UCSC genome browser. 'ci' corresponds to the binding site estimates +/-3*se, while 'fixed' corresponds to the binding site estimates +/-3*length. 'bed' and 'wig' files can be exported using the 'export' function fo the 'rtracklayer' package.
}
\value{
An object of type 'RangedData'.
}
\references{Xuekui Zhang, Gordon Robertson, Sangsoon Woo, Brad G. Hoffman, and Raphael Gottardo, "Probabilistic Inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data" GenomeBiology, under review.
}
\author{
  Xuekui Zhang, \email{ubcxzhang@gmail.com} 
  Sangsoon Woo, \email{swoo@fhcrc.org} and
  Raphael Gottardo, \email{raphael.gottardo@ircm.qc.ca}
}
\seealso{export}
\examples{


\dontrun{
  rdBed<-makeRangedDataOutput(ping,type="bed",filter=list(delta=c(50,Inf),se=c(0,50),sigmaSqF=c(0,22500),sigmaSqR=c(0,22500),score=c(10,Inf)))
  export(rbBed,"myfile.bed")
  rdBed<-makeRangedDataOutput(ping,type="wig",filter=list(delta=c(50,Inf),se=c(0,50),sigmaSqF=c(0,22500),sigmaSqR=c(0,22500),score=c(10,Inf)))
  export(rbBed,"myfile.wig")}
  
}


\keyword{process}
\keyword{data}