NuPoP-package {NuPoP} | R Documentation |
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.
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.
Ji-Ping Wang, Liqun Xi
Maintainer: Ji-Ping Wang<jzwang@northwestern.edu>
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
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)