HIREewas

DOI: 10.18129/B9.bioc.HIREewas    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see HIREewas.

Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies

Bioconductor version: 3.9

In epigenome-wide association studies, the measured signals for each sample are a mixture of methylation profiles from different cell types. The current approaches to the association detection only claim whether a cytosine-phosphate-guanine (CpG) site is associated with the phenotype or not, but they cannot determine the cell type in which the risk-CpG site is affected by the phenotype. We propose a solid statistical method, HIgh REsolution (HIRE), which not only substantially improves the power of association detection at the aggregated level as compared to the existing methods but also enables the detection of risk-CpG sites for individual cell types. The "HIREewas" R package is to implement HIRE model in R.

Author: Xiangyu Luo <xyluo1991 at gmail.com>, Can Yang <macyang at ust.hk>, Yingying Wei <yweicuhk at gmail.com>

Maintainer: Xiangyu Luo <xyluo1991 at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("HIREewas")

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("HIREewas")

 

PDF	R Script	HIREewas
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, DifferentialMethylation, FeatureExtraction, Software
Version	1.2.1
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
License	GPL (>= 2)
Depends	R (>= 3.5.0)
Imports	quadprog, gplots, grDevices, stats
LinkingTo
Suggests	BiocStyle, knitr, BiocGenerics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	HIREewas_1.2.1.tar.gz
Windows Binary	HIREewas_1.2.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	HIREewas_1.2.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HIREewas
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HIREewas
Package Short Url	https://bioconductor.org/packages/HIREewas/
Package Downloads Report	Download Stats