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HIREewas

This is the development version of HIREewas; for the stable release version, see HIREewas.

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


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
HIREewas PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, DifferentialMethylation, FeatureExtraction, Software
Version 1.21.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL (>= 2)
Depends R (>= 3.5.0)
Imports quadprog, gplots, grDevices, stats
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Suggests BiocStyle, knitr, BiocGenerics
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Package Archives

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

Source Package HIREewas_1.21.0.tar.gz
Windows Binary HIREewas_1.21.0.zip
macOS Binary (x86_64) HIREewas_1.21.0.tgz
macOS Binary (arm64) HIREewas_1.21.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/HIREewas
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HIREewas
Bioc Package Browser https://code.bioconductor.org/browse/HIREewas/
Package Short Url https://bioconductor.org/packages/HIREewas/
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