Package: methylclock 1.99.2

Dolors Pelegri-Siso

methylclock: Chronological, Gestational and Biological DNAm Age Estimation with Methylation-Based Clocks

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.

Authors:Dolors Pelegri-Siso [aut, cre], Juan R. Gonzalez [aut]

# Install 'methylclock' in R:

install.packages('methylclock', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/isglobal-brge/methylclock/issues

Uses libs:

openblas– Optimized BLAS
curl– Easy-to-use client-side URL transfer library
openssl– Secure Sockets Layer toolkit
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

clock_catalog - Catalogue of the clocks in the package
methylclock_betas - Example methylation beta matrix
methylclock_cells - Clock estimates with blood cell proportions
methylclock_demo - Example clock estimates for a public blood cohort
methylclock_longitudinal - A longitudinal example: children sampled repeatedly from birth to age 3
methylclock_references - Clock estimates on the shipped reference cohorts
methylclock_smoking - Smoking predictor scores with smoking status
methylclock_validation - Clock estimates on two independent validation cohorts

On BioConductor:methylclock-1.99.1(bioc 3.24)methylclock-1.18.0(bioc 3.23)

dnamethylation biologicalquestion preprocessing statisticalmethod normalization openblas curl openssl cpp openmp

7.56 score 55 stars 83 scripts 786 downloads 49 exports 78 dependencies

Last updated from:30be028406. Checks:1 WARNING, 14 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	1166
linux-devel-arm64	OK	296
linux-devel-x86_64	OK	392
source / vignettes	OK	1429
linux-release-arm64	OK	1196
linux-release-x86_64	OK	1354
macos-release-arm64	OK	189
macos-release-x86_64	OK	671
macos-oldrel-arm64	OK	263
macos-oldrel-x86_64	OK	498
windows-devel-arm64	OK	344
windows-devel-x86_64	OK	432
windows-release-arm64	OK	461
windows-release-x86_64	OK	365
windows-oldrel-x86_64	OK	335
wasm-release	FAIL	1194

Exports:ageAcceleration ageAccelerationChen altumage_forward anti_trafo cellCounts clock_info clock_list clock_predictors clock_register clock_registry clock_reset clock_statuses clock_targets clockAccuracy clockCoverage clockTrajectories compute_clocks DNAmAge DNAmGA EEAA IEAA imputeKNN listCellReferences mc_to_hdf5 mcd_backends mcd_cache_clear mcd_manifest mcd_resource mcd_resource_file methylclock new_methylclock normalize_coef persist plotAccelerationByGroup plotAgeAcceleration plotBlandAltman plotClockCorrelation plotClockDensities plotClockDistributions plotDNAmAge plotGroupDifference plotReferenceRange plotSampleDiscordance plotSamplePCA plotTrajectories qcReport sampleQC theme_methylclock trajectoryRates

Dependencies:AnnotationDbi AnnotationHub askpass BH BigDataStatMeth Biobase BiocBaseUtils BiocFileCache BiocGenerics biocmake BiocManager BiocVersion Biostrings bit bit64 bitops blob cachem cli cpp11 crayon curl data.table DBI dbplyr dir.expiry dplyr ExperimentHub farver fastmap filelock generics ggplot2 glue gtable httr httr2 IRanges isoband jsonlite KEGGREST labeling lifecycle magrittr memoise mime openssl pillar pkgconfig png preprocessCore purrr quadprog R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl Rhdf5lib rlang RSQLite S4Vectors S7 scales Seqinfo stringi stringr sys tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector yaml

Estimating DNA methylation age with methylclock

Rendered frommethylclock.Rmdusingknitr::rmarkdown

Last update: 2026-09-09
Started: 2019-03-15

Help page	Topics
Epigenetic age acceleration, intrinsic and extrinsic	ageAcceleration
Chen-style extrinsic age acceleration with data-driven weights	ageAccelerationChen
Horvath age transformation (inverse)	anti_trafo
Coerce a methylclock result to a data frame	as.data.frame.methylclock
Estimate blood cell-type proportions from methylation	cellCounts
Catalogue of the clocks in the package	clock_catalog
Look up one clock's registry entry	clock_info
List and filter registered clocks	clock_list
Supported prediction engines	clock_predictors
Register a clock	clock_register
The clock registry	clock_registry
Clear the clock registry	clock_reset
Availability status labels	clock_statuses
Supported biological targets	clock_targets
How well each clock tracks chronological age	clockAccuracy
CpG coverage of each clock in a dataset	clockCoverage
Arrange repeated samples into per-subject clock trajectories	clockTrajectories
Estimate clocks from a methylation matrix	compute_clocks
Estimate chronological and biological DNAm age	DNAmAge
Estimate gestational DNAm age	DNAmGA
Extrinsic epigenetic age acceleration (canonical EEAA)	EEAA
Intrinsic epigenetic age acceleration (canonical IEAA)	IEAA
KNN-impute a methylation matrix	imputeKNN
Cell-type reference panels available for deconvolution	listCellReferences
Store a methylation matrix on disk as HDF5	mc_to_hdf5
Configure the resource backend chain	mcd_backends
Clear the resource cache	mcd_cache_clear
The resource manifest	mcd_manifest
Resolve a clock resource by identifier	mcd_resource
Resolve a file resource to a local path	mcd_resource_file
Estimate DNA methylation clocks	methylclock
Example methylation beta matrix	methylclock_betas
Clock estimates with blood cell proportions	methylclock_cells
Example clock estimates for a public blood cohort	methylclock_demo
A longitudinal example: children sampled repeatedly from birth to age 3	methylclock_longitudinal
Clock estimates on the shipped reference cohorts	methylclock_references
Smoking predictor scores with smoking status	methylclock_smoking
Clock estimates on two independent validation cohorts	methylclock_validation
Construct a methylclock result	new_methylclock
Normalize a coefficient resource to canonical form	normalize_coef
Persist a result to a file	persist persist.methylclock
Plot epigenetic age acceleration by a sample group	plotAccelerationByGroup
Plot epigenetic age acceleration	plotAgeAcceleration
Bland-Altman plot of predicted vs. chronological age	plotBlandAltman
Heatmap of the correlation between clocks	plotClockCorrelation
Plot the density of each clock's estimates, optionally split by a group	plotClockDensities
Plot the distribution of each clock's estimates	plotClockDistributions
Plot predicted epigenetic age against chronological age	plotDNAmAge
Plot the per-clock difference between two groups as a forest plot	plotGroupDifference
Plot samples against the percentile bands of a reference cohort	plotReferenceRange
Plot how much the clocks agree on each sample	plotSampleDiscordance
PCA of samples in clock space	plotSamplePCA
Plot each subject's clock trajectory over age	plotTrajectories
Quality-control report for clock estimates	qcReport
Per-sample quality control	sampleQC
A clean theme for methylclock plots	theme_methylclock
Each subject's rate of epigenetic aging, clock by clock	trajectoryRates

Package: methylclock 1.99.2

methylclock: Chronological, Gestational and Biological DNAm Age Estimation with Methylation-Based Clocks

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