\name{segmentReads} 
\alias{segmentReads} 


\title{Segment the genome into candidate regions} 
\description{ 
    Pre-process bidirectional aligned reads data from a single ChIP-Seq experiment to detect candidate regions with a minimum number of forward and reverse reads. These candidate regions will then be processed by PICS.}
\usage{
segmentReads(data, dataC=NULL, map=NULL,minReads=2, minReadsInRegion=3,jitter=FALSE, dataType="TF",maxLregion=0,minLregion=100)
}


\arguments{
  \item{data}{A `GenomeData' object containing the IP reads. See details for more information on how to set up the data.}
  \item{dataC}{A `GenomeData' object containing the control reads. Set to NULL by default, i.e. no control.}
  \item{map}{A `RangedData' object containing the mappability profiles. Set to NULL by default, i.e. no profiles.}
  \item{minReads}{The minimum number of F/R reads to be present in the sliding window.}
  \item{minReadsInRegion}{The minimum number of F/R reads to be present in the region.}
  \item{jitter}{A logical value stating whether some noise should be added to the read locations. This is recommended if the read positions have lots of duplicates.}
   \item{dataType}{Type of experiment.}
\item{maxLregion}{The maximum length.}
\item{minLregion}{The minimum length.}
}

\value{
An object of class `segmentReadsList' containing the results for all regions pre-processed. 
}
\references{
X. Zhang, G. Robertson, M. Krzywinski, K. Ning, A. Droit, S. Jones, and R. Gottardo, ``PICS: Probabilistic Inference for ChIP-seq" arXiv, 0903.3206, 2009.
}
\author{Xuekui Zhang and Raphael Gottardo <\email{raphael.gottardo@ircm.qc.ca}>}

\seealso{segmentReads}
\seealso{picsFDR}
\examples{
# Read data
path<-system.file("extdata",package="PICS")
## Note that the col name for the chromosome needs to be space and not chr
dataIP<-read.table(file.path(path,"Treatment_tags_chr21_sort.bed"),header=TRUE,colClasses=c("factor","integer","integer","factor"))
dataIP<-as(dataIP,"RangedData")
dataIP<-as(dataIP,"GenomeData")

dataCont<-read.table(file.path(path,"Input_tags_chr21_sort.bed"),header=TRUE,colClasses=c("factor","integer","integer","factor"))
dataCont<-as(dataCont,"RangedData")
dataCont<-as(dataCont,"GenomeData")

map<-read.table(file.path(path,"mapProfileShort"),header=TRUE,colClasses=c("factor","integer","integer","NULL"))
map<-as(map,"RangedData")
## Remove the chrM
map<-map[-23]
seg<-segmentReads(dataIP, dataC=dataCont, map=map, minReads=1)
}

\keyword{data}
\keyword{models}