\name{getPermutatedWinScores}
\alias{getPermutatedWinScores}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Obtain the read-enrichment score distribution under the null hypothesis }
\description{
 Obtain the read-enrichment score distribution under the null hypothesis 
}
\usage{
getPermutatedWinScores(file, nn)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{file}{ Name of the file generated by permutatedWinScores }
  \item{nn}{ ID for the multiple permutation process }
  
}

\value{
Numeric vector of score values under permutation
}
\references{ Muino et al. (submitted). Plant ChIP-seq Analyzer: An R package for the statistcal detection of protein-bound genomic regions. \cr Kaufmann et al.(2009).Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PLoS Biology; 7(4):e1000090.}
\author{ Jose M Muino, \email{jose.muino@wur.nl}}

\seealso{CSAR-package, permutatedWinScores}
\examples{

##For this example we will use the a subset of the SEP3 ChIP-seq data (Kaufmann, 2009)
data("CSAR-dataset");
##We calculate the number of hits for each nucleotide posotion for the control and sample. We do that just for chromosome chr1, and for positions 1 to 10kb
nhitsS<-mappedReads2Nhits(sampleSEP3_test,file="sampleSEP3_test",chr=c("CHR1v01212004"),chrL=c(10000))
nhitsC<-mappedReads2Nhits(controlSEP3_test,file="controlSEP3_test",chr=c("CHR1v01212004"),chrL=c(10000))


##We calculate two sets of read-enrichment scores through permutation
permutatedWinScores(nn=1,sample=sampleSEP3_test,control=controlSEP3_test,fileOutput="test",chr=c("CHR1v01212004"),chrL=c(100000))
permutatedWinScores(nn=2,sample=sampleSEP3_test,control=controlSEP3_test,fileOutput="test",chr=c("CHR1v01212004"),chrL=c(100000))

###Next function will get all permutated score values generated by permutatedWinScores function. 
##This represent the score distribution under the null hypotesis and therefore it can be use to control the error of our test.
nulldist<-getPermutatedWinScores(file="test",nn=1:2)

}