NuPoP-package {NuPoP} | R Documentation

## An R package for nucleosome positioning prediction

### Description

`NuPoP` is an R package for `Nu`cleosome `Po`sitioning `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 `predNuPoP`, `readNuPoP`, and `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

Package: | NuPoP
Type: | Package
Version: | 1.0
Date: | 2010-06-24
License: | GPL-2

`predNuPoP`: R function invoking Fortran codes to predict nucleosome positioning, nucleosome occupancy and binding affinity.

`readNuPoP`: R function to read in the prediction results by `predNuPoP`.

`plotNuPoP`: R function to visualize predictions.

`predNuPoP_chem`: R function invoking Fortran codes to predict nucleosome positioning, nucleosome occupancy and binding affinity using profiles trained based on chemically mapped nucleosomes in yeast, S.pombe, mouse and human.

### Author(s)

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

    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)

[Package NuPoP version 2.0.0 Index]