An R package for nucleosome positioning prediction

Description

NuPoP is an R package for Nucleosome Positioning Prediction. 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

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.

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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(NuPoP)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/NuPoP/NuPoP-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: NuPoP-package
> ### Title: An R package for nucleosome positioning prediction
> ### Aliases: NuPoP-package NuPoP
> 
> ### ** Examples
> 
> library(NuPoP)
> predNuPoP(system.file("extdata", "test.seq", package="NuPoP"),species=7,model=4)
Prediction output: '/home/ddbj/DataUpdator-rgm3/target/test.seq_Prediction4.txt'> 
> ## 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>