methylclock
This is the development version of methylclock; for the stable release version, see methylclock.
Chronological, Gestational and Biological DNAm Age Estimation with Methylation-Based Clocks
Bioconductor version: Development (3.24)
Estimates chronological, gestational and biological DNA methylation (DNAm) age, trait scores and epigenetic age acceleration from methylation beta values. Implements 44 published clocks, selectable by name, family or array platform: chronological (Horvath, Hannum, BNN, skin+blood, PedBE, Wu, AltumAge and others, including the cross-platform Garma clock native to EPICv2), gestational (Knight, Bohlin, Mayne, Lee, NEOage), phenotypic and pace-of-aging (Levine, DunedinPACE), telomere length, mitotic counters (epiTOC1/epiTOC2, HypoClock, stemTOC, RepliTali), causal (CausAge, DamAge, AdaptAge) and trait EpiScores. Accepts matrices, data frames, Bioconductor containers or HDF5 files, computing block-wise out-of-core through BigDataStatMeth when the data exceed memory. Provides configurable missing-value imputation (mean, reference or KNN), cell-type deconvolution, intrinsic and extrinsic epigenetic age acceleration (IEAA, EEAA), quality-control reports and plotting functions.
Author: Dolors Pelegri-Siso [aut, cre]
, Juan R. Gonzalez [aut]
, Carlos Ruiz-Arenas [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri at isglobal.org>
citation("methylclock")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("methylclock")
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("methylclock")| Estimating DNA methylation age with methylclock | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiologicalQuestion, DNAMethylation, Normalization, Preprocessing, Software, StatisticalMethod |
| Version | 1.99.1 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.3.0) |
| Imports | utils, stats, preprocessCore, Rcpp, BigDataStatMeth, ExperimentHub, ggplot2, rlang, quadprog |
| System Requirements | GNU make, C++17 |
| URL | https://github.com/isglobal-brge/methylclock |
| Bug Reports | https://github.com/isglobal-brge/methylclock/issues |
See More
| Suggests | testthat (>= 3.0.0), digest, impute, knitr, rmarkdown, BiocStyle, kableExtra, minfi, Biobase, SummarizedExperiment |
| Linking To | Rcpp, RcppEigen, Rhdf5lib, BigDataStatMeth, BH |
| 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 | methylclock_1.99.1.tar.gz |
| Windows Binary (x86_64) | methylclock_1.19.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | methylclock_1.99.1.tgz |
| macOS Binary (sonoma-arm64) | methylclock_1.99.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/methylclock |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/methylclock |
| Bioc Package Browser | https://code.bioconductor.org/browse/methylclock/ |
| Package Short Url | https://bioconductor.org/packages/methylclock/ |
| Package Downloads Report | Download Stats |