\name{NuPoP-package}
\alias{NuPoP-package}
\alias{NuPoP}
\docType{package}
\title{
 An R package for nucleosome positioning prediction
}
\description{
\code{NuPoP} is an R package for \code{Nu}cleosome \code{Po}sitioning \code{P}rediction.
This package is built upon a duration hidden Markov model proposed in Xi et al 2010 and 
Wang et al 2008. The core of the package was written in Fortran. Three functions  including \code{predNuPoP}, \code{readNuPoP}, 
and \code{plotNuPoP} are provided for nucleosome positioning prediction, prediction results readin, and prediction results visualization respectively. 
The input DNA sequence can be of any length.
}
\details{
\tabular{ll}{
Package: \tab NuPoP\cr
Type: \tab Package\cr
Version: \tab 1.0\cr
Date: \tab 2010-06-24\cr
License: \tab  GPL-2\cr
}
\code{predNuPoP}: R function invoking Fortran codes to predict nucleosome positioning, nucleosome occupancy and binding affinity.

\code{readNuPoP}: R function to read in the prediction results by \code{predNuPoP}.

\code{plotNuPoP}: R function to visualize predictions.
}
\author{
Ji-Ping Wang, Liqun Xi

Maintainer: Ji-Ping Wang<jzwang@northwestern.edu>
}
\references{
Xi, L., Fondufe-Mittendorf, Y., Xia, L., Flatow, J., Widom, J. and Wang, J.-P. (2010), Predicting nucleosome positioning using a duration Hidden Markov Model, BMC Bioinformatics , doi:10.1186/1471-2105-11-346

Wang, J.-P., Fondufe-Mittendorf, Y., Xi, L., Tsai, G., Segal, E. and Widom, J.(2008), Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae, PLoS Computational Biology, 4(9) e1000175
}

\examples{
library(NuPoP)
predNuPoP(system.file("extdata", "test.seq", package="NuPoP"),species=7,model=4)

## the prediction results are stored in the current working directory
## the user should replace "system.file("extdata","test.seq_Prediction4.txt",package="NuPoP")"
## by the actual path and file name generated from prediction.

temp=readNuPoP(system.file("extdata","test.seq_Prediction4.txt",package="NuPoP"),startPos=1,endPos=5000)
plotNuPoP(temp)
}