To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BPRMeth")

In most cases, you don't need to download the package archive at all.

BPRMeth

 

Model higher-order methylation profiles

Bioconductor version: Release (3.5)

BPRMeth package uses the Binomial Probit Regression likelihood to model methylation profiles and extract higher order features. These features quantitate precisely notions of shape of a methylation profile. Using these higher order features across promoter-proximal regions, we construct a powerful predictor of gene expression. Also, these features are used to cluster proximal-promoter regions using the EM algorithm.

Author: Chantriolnt-Andreas Kapourani [aut, cre]

Maintainer: Chantriolnt-Andreas Kapourani <kapouranis.andreas at gmail.com>

Citation (from within R, enter citation("BPRMeth")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BPRMeth")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BPRMeth")

 

PDF R Script An Introduction to the BPR method
PDF   Reference Manual
Text   NEWS

Details

biocViews Bayesian, Clustering, Coverage, DNAMethylation, Epigenetics, FeatureExtraction, GeneExpression, GeneRegulation, Genetics, KEGG, RNASeq, Regression, Sequencing, Software
Version 1.2.0
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
License GPL-3
Depends R (>= 3.3.0), GenomicRanges
Imports assertthat, methods, MASS, doParallel, parallel, e1071, earth, foreach, randomForest, stats, IRanges, S4Vectors, data.table, graphics
LinkingTo
Suggests testthat, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source BPRMeth_1.2.0.tar.gz
Windows Binary BPRMeth_1.2.0.zip
Mac OS X 10.11 (El Capitan) BPRMeth_1.2.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/BPRMeth/tree/release-3.5
Package Short Url http://bioconductor.org/packages/BPRMeth/
Package Downloads Report Download Stats

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