HIREewas
Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies
Bioconductor version: Release (3.20)
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("HIREewas")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("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")| HIREewas | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, DifferentialMethylation, FeatureExtraction, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (6 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.5.0) |
| Imports | quadprog, gplots, grDevices, stats |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, BiocGenerics |
| 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 | HIREewas_1.24.0.tar.gz |
| Windows Binary (x86_64) | HIREewas_1.24.0.zip (64-bit only) |
| macOS Binary (x86_64) | HIREewas_1.24.0.tgz |
| macOS Binary (arm64) | HIREewas_1.23.0.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/ |
| Package Downloads Report | Download Stats |