BPRMeth

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see BPRMeth.

Model higher-order methylation profiles

Bioconductor version: 3.6

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 (version "3.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BPRMeth")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("BPRMeth")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, Clustering, Coverage, DNAMethylation, Epigenetics, FeatureExtraction, GeneExpression, GeneRegulation, Genetics, KEGG, RNASeq, Regression, Sequencing, Software
Version	1.4.0
In Bioconductor since	BioC 3.4 (R-3.3) (7.5 years)
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
System Requirements
URL

Suggests	testthat, knitr, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	BPRMeth_1.4.0.tar.gz
Windows Binary	BPRMeth_1.4.0.zip
Mac OS X 10.11 (El Capitan)	BPRMeth_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BPRMeth
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BPRMeth
Package Short Url	https://bioconductor.org/packages/BPRMeth/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive