Package 'methylclockData'

Title: Data for methylclock package
Description: Data resources used by the methylclock package to estimate chronological, gestational and biological age from DNA methylation, and to adjust those estimates for blood cell composition. It provides the coefficient tables of the individual clocks, the CpG sets of the mitotic counters, the weights of the neural network clock, and example methylation datasets. It also provides nine cell type reference datasets (andrews and bakulski cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete, combined cord blood, cord blood gse68456, gervin and lyle cord blood, guintivano dlpfc, saliva gse48472), downloaded from meffil (https://github.com/perishky/meffil/), which are used to estimate cell counts for the extrinsic epigenetic age acceleration (EEAA) method. All resources are served through ExperimentHub.
Authors: Juan R. Gonzalez [aut], Dolors Pelegri-Siso [aut, cre]
Maintainer: Dolors Pelegri-Siso <[email protected]>
License: MIT + file LICENSE
Version: 1.21.4
Built: 2026-10-10 10:42:08 UTC
Source: https://github.com/bioc/methylclockData

Help Index

coefAdaptAge

Description

Coefficients AdaptAge adaptive causal clock. 998 CpGs described in Ying et al. (2024).

Usage

get_coefAdaptAge()

Details

get_coefAdaptAge retrieves this resource from ExperimentHub.

Value

coefAdaptAge dataset

Examples

get_coefAdaptAge()

coefAltumAge

Description

AltumAge neural network weights and scaler. Layer weights and input scaler of the AltumAge neural network, from de Lima Camillo et al. (2022).

Usage

get_coefAltumAge()

Details

get_coefAltumAge retrieves this resource from ExperimentHub.

Value

path to the coefAltumAge file in the local cache

Examples

get_coefAltumAge()

coefAltumAgeRef

Description

AltumAge input CpG order. The input CpG identifiers in the order the AltumAge network expects, from de Lima Camillo et al. (2022).

Usage

get_coefAltumAgeRef()

Details

get_coefAltumAgeRef retrieves this resource from ExperimentHub.

Value

coefAltumAgeRef dataset

Examples

get_coefAltumAgeRef()

coefBLUP

Description

get_coefBLUP returns the Best Linear Unbiased Prediction (BLUP) clock coefficients

Usage

get_coefBLUP()

Value

coefBLUP dataset

Examples

get_coefBLUP()

coefBohlin

Description

get_coefBohlin returns the Bohlin's clock coefficients

Usage

get_coefBohlin()

Value

coefBohlin dataset

Examples

get_coefBohlin()

coefCausAge

Description

Coefficients CausAge causal clock. 581 CpGs described in Ying et al. (2024).

Usage

get_coefCausAge()

Details

get_coefCausAge retrieves this resource from ExperimentHub.

Value

coefCausAge dataset

Examples

get_coefCausAge()

coefDamAge

Description

Coefficients DamAge damaging causal clock. 1089 CpGs described in Ying et al. (2024).

Usage

get_coefDamAge()

Details

get_coefDamAge retrieves this resource from ExperimentHub.

Value

coefDamAge dataset

Examples

get_coefDamAge()

coefDunedinPACE

Description

Coefficients DunedinPACE pace-of-aging estimator. 173 CpGs described in Belsky (2022).

Usage

get_coefDunedinPACE()

Details

get_coefDunedinPACE retrieves this resource from ExperimentHub.

Value

coefDunedinPACE dataset

Examples

get_coefDunedinPACE()

coefDunedinPACEGS

Description

DunedinPACE reference means for probe normalization. Reference probe means used to normalize the DunedinPACE input, from Belsky (2022).

Usage

get_coefDunedinPACEGS()

Details

get_coefDunedinPACEGS retrieves this resource from ExperimentHub.

Value

coefDunedinPACEGS dataset

Examples

get_coefDunedinPACEGS()

coefEN

Description

get_coefEN returns the Elastic Net (EN) clock coefficients

Usage

get_coefEN()

Value

coefEN dataset

Examples

get_coefEN()

coefEPIC

Description

get_coefEPIC returns the EPIC clock coefficients

Usage

get_coefEPIC()

Value

coefEPIC dataset

Examples

get_coefEPIC()

coefEpiTOC1

Description

CpG set for the epiTOC1 mitotic counter. 385 CpGs described in Yang et al. (2016).

Usage

get_coefEpiTOC1()

Details

get_coefEpiTOC1 retrieves this resource from ExperimentHub.

Value

coefEpiTOC1 dataset

Examples

get_coefEpiTOC1()

coefEpiTOC2

Description

Parameters for the epiTOC2 mitotic counter. 163 CpGs described in Teschendorff (2020).

Usage

get_coefEpiTOC2()

Details

get_coefEpiTOC2 retrieves this resource from ExperimentHub.

Value

coefEpiTOC2 dataset

Examples

get_coefEpiTOC2()

coefGarma

Description

Coefficients Garma cross-platform age clock. 4962 CpGs described in Garma (2024); includes squared-beta terms (power column). Trained on probes shared by the 450K, EPICv1 and EPICv2 arrays. Licence CC BY-NC-ND 4.0.

Usage

get_coefGarma()

Details

get_coefGarma retrieves this resource from ExperimentHub.

Value

coefGarma dataset

Examples

get_coefGarma()

coefHannum

Description

get_coefHannum returns the Hannum's clock coefficients

Usage

get_coefHannum()

Value

coefHannum dataset

Examples

get_coefHannum()

coefHorvath

Description

get_coefHorvath returns the Hobarth's clock coefficients

Usage

get_coefHorvath()

Value

coefHorvath dataset

Examples

get_coefHorvath()

coefHypoClock

Description

CpG set for the HypoClock solo-WCGW counter. 678 CpGs described in Teschendorff (2020).

Usage

get_coefHypoClock()

Details

get_coefHypoClock retrieves this resource from ExperimentHub.

Value

coefHypoClock dataset

Examples

get_coefHypoClock()

coefKnightGA

Description

get_coefKnightGA returns the Knight's clock coefficients

Usage

get_coefKnightGA()

Value

coefKnightGA dataset

Examples

get_coefKnightGA()

coefLeeGA

Description

get_coefLeeGA returns the Lee's Gestational Age clock coefficients

Usage

get_coefLeeGA()

Value

coefLeeGA dataset

Examples

get_coefLeeGA()

coefLevine

Description

get_coefLevine returns the Levine's clock coefficients

Usage

get_coefLevine()

Value

coefLevine dataset

Examples

get_coefLevine()

coefLin

Description

Coefficients Lin blood clock. 99 CpGs described in Lin et al. (2016).

Usage

get_coefLin()

Details

get_coefLin retrieves this resource from ExperimentHub.

Value

coefLin dataset

Examples

get_coefLin()

coefMayneGA

Description

get_coefMayneGA returns the Mayne's clock coefficients

Usage

get_coefMayneGA()

Value

coefMayneGA dataset

Examples

get_coefMayneGA()

coefMcCartneyAlcohol

Description

Coefficients McCartney alcohol EpiScore. 450 CpGs described in McCartney et al. (2018).

Usage

get_coefMcCartneyAlcohol()

Details

get_coefMcCartneyAlcohol retrieves this resource from ExperimentHub.

Value

coefMcCartneyAlcohol dataset

Examples

get_coefMcCartneyAlcohol()

coefMcCartneyBMI

Description

Coefficients McCartney body mass index EpiScore. 1109 CpGs described in McCartney et al. (2018).

Usage

get_coefMcCartneyBMI()

Details

get_coefMcCartneyBMI retrieves this resource from ExperimentHub.

Value

coefMcCartneyBMI dataset

Examples

get_coefMcCartneyBMI()

coefMcCartneyBodyFat

Description

Coefficients McCartney body fat EpiScore. 968 CpGs described in McCartney et al. (2018).

Usage

get_coefMcCartneyBodyFat()

Details

get_coefMcCartneyBodyFat retrieves this resource from ExperimentHub.

Value

coefMcCartneyBodyFat dataset

Examples

get_coefMcCartneyBodyFat()

coefMcCartneyEducation

Description

Coefficients McCartney education EpiScore. 373 CpGs described in McCartney et al. (2018).

Usage

get_coefMcCartneyEducation()

Details

get_coefMcCartneyEducation retrieves this resource from ExperimentHub.

Value

coefMcCartneyEducation dataset

Examples

get_coefMcCartneyEducation()

coefMcCartneyHDL

Description

Coefficients McCartney HDL cholesterol EpiScore. 737 CpGs described in McCartney et al. (2018).

Usage

get_coefMcCartneyHDL()

Details

get_coefMcCartneyHDL retrieves this resource from ExperimentHub.

Value

coefMcCartneyHDL dataset

Examples

get_coefMcCartneyHDL()

coefMcCartneyLDL

Description

Coefficients McCartney LDL cholesterol EpiScore. 233 CpGs described in McCartney et al. (2018).

Usage

get_coefMcCartneyLDL()

Details

get_coefMcCartneyLDL retrieves this resource from ExperimentHub.

Value

coefMcCartneyLDL dataset

Examples

get_coefMcCartneyLDL()

coefMcCartneySmoking

Description

Coefficients McCartney smoking EpiScore. 233 CpGs described in McCartney et al. (2018).

Usage

get_coefMcCartneySmoking()

Details

get_coefMcCartneySmoking retrieves this resource from ExperimentHub.

Value

coefMcCartneySmoking dataset

Examples

get_coefMcCartneySmoking()

coefMcCartneyTotalChol

Description

Coefficients McCartney total cholesterol EpiScore. 204 CpGs described in McCartney et al. (2018).

Usage

get_coefMcCartneyTotalChol()

Details

get_coefMcCartneyTotalChol retrieves this resource from ExperimentHub.

Value

coefMcCartneyTotalChol dataset

Examples

get_coefMcCartneyTotalChol()

coefMcCigarette

Description

Coefficients mCigarette smoking score. 1255 CpGs described in Chybowska et al. (2025).

Usage

get_coefMcCigarette()

Details

get_coefMcCigarette retrieves this resource from ExperimentHub.

Value

coefMcCigarette dataset

Examples

get_coefMcCigarette()

coefNEOaPMA450K

Description

Coefficients NEOage post-menstrual age clock (450K). 408 CpGs described in Graw et al. (2021).

Usage

get_coefNEOaPMA450K()

Details

get_coefNEOaPMA450K retrieves this resource from ExperimentHub.

Value

coefNEOaPMA450K dataset

Examples

get_coefNEOaPMA450K()

coefNEOaPMAEPIC

Description

Coefficients NEOage post-menstrual age clock (EPIC). 520 CpGs described in Graw et al. (2021).

Usage

get_coefNEOaPMAEPIC()

Details

get_coefNEOaPMAEPIC retrieves this resource from ExperimentHub.

Value

coefNEOaPMAEPIC dataset

Examples

get_coefNEOaPMAEPIC()

coefNEOaPNA450K

Description

Coefficients NEOage post-natal age clock (450K). 302 CpGs described in Graw et al. (2021).

Usage

get_coefNEOaPNA450K()

Details

get_coefNEOaPNA450K retrieves this resource from ExperimentHub.

Value

coefNEOaPNA450K dataset

Examples

get_coefNEOaPNA450K()

coefNEOaPNAEPIC

Description

Coefficients NEOage post-natal age clock (EPIC). 508 CpGs described in Graw et al. (2021).

Usage

get_coefNEOaPNAEPIC()

Details

get_coefNEOaPNAEPIC retrieves this resource from ExperimentHub.

Value

coefNEOaPNAEPIC dataset

Examples

get_coefNEOaPNAEPIC()

coefPedBE

Description

get_coefPedBE returns the PedBE's clock coefficients

Usage

get_coefPedBE()

Value

coefPedBE dataset

Examples

get_coefPedBE()

coefRepliTali

Description

Coefficients RepliTali mitotic clock. 87 CpGs described in Endicott et al. (2022).

Usage

get_coefRepliTali()

Details

get_coefRepliTali retrieves this resource from ExperimentHub.

Value

coefRepliTali dataset

Examples

get_coefRepliTali()

coefSkin

Description

get_coefSkin returns the Horvath's skin+blood clock coefficients

Usage

get_coefSkin()

Value

coefSkin dataset

Examples

get_coefSkin()

coefStemTOC

Description

CpG set for the stemTOC mitotic counter. 371 CpGs described in Zhu et al. (2024).

Usage

get_coefStemTOC()

Details

get_coefStemTOC retrieves this resource from ExperimentHub.

Value

coefStemTOC dataset

Examples

get_coefStemTOC()

coefTL

Description

get_coefTL returns the Telomere Length clock coefficients

Usage

get_coefTL()

Value

coefTL dataset

Examples

get_coefTL()

coefVidalBralo

Description

Coefficients Vidal-Bralo blood clock. 8 CpGs described in Vidal-Bralo et al. (2016).

Usage

get_coefVidalBralo()

Details

get_coefVidalBralo retrieves this resource from ExperimentHub.

Value

coefVidalBralo dataset

Examples

get_coefVidalBralo()

coefWeidner

Description

Coefficients Weidner three-CpG clock. 3 CpGs described in Weidner et al. (2014).

Usage

get_coefWeidner()

Details

get_coefWeidner retrieves this resource from ExperimentHub.

Value

coefWeidner dataset

Examples

get_coefWeidner()

Wu

Description

get_coefWu returns the Wu's clock coefficients

Usage

get_coefWu()

Value

Wu dataset

Examples

get_coefWu()

cpgs_bn

Description

get_cpgs_bn returns data to use Horvath's CpGs to train a Bayesian Neural Network (BNN)

Usage

get_cpgs_bn()

Value

cpgs_bn dataset

Examples

get_cpgs_bn()

MethylationDataExample55

Description

get_MethylationDataExample MethylationDataExample55 for vignette

Usage

get_MethylationDataExample()

Value

MethylationDataExample55 dataset

Examples

get_MethylationDataExample()

probeAnnotation21kdatMethUsed

Description

get_probeAnnotation21kdatMethUsed returns probeAnnotation21kdatMethUsed

Usage

get_probeAnnotation21kdatMethUsed()

Value

probeAnnotation21kdatMethUsed dataset

Examples

get_probeAnnotation21kdatMethUsed()

references

Description

The methylclockData package is a repository of a few public datasets that needs the *methylclock* package to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks.

Usage

get_references()

Format

A list with different data frame.

blood gse35069 complete

methylation profiles from Reinius 2012 for purified blood cell types. It includes CD4T, CD8T, Mono,

blood gse35069

methylation profiles from Reinius 2012 for purified blood cell types. It includes CD4T,CD8T, Mono, Bcell, NK and Gran.

blood gse35069 chen

methylation profiles from Chen 2017 blood cell types. It includes CD4T, CD8T, Mono, Bcell, NK, Neu and Eos.

andrews and bakulski cord blood

Cord blood reference from Bakulski 2016. It includes Bcell, CD4T, CD8T, Gran, Mono, NK and nRBC.

cord blood gse68456

Cord blood methylation profiles from De 2015. It includes CD4T, CD8T, Mono, Bcell, NK, Neu, Eos and RBC.

gervin and lyle cord blood

Cord blood reference generated by Kristina Gervin and Robert Lyle, available at 'miffil' package. It includes CD14, Bcell, CD4T, CD8T, NK, Gran.

saliva gse48472

Reference generated from the multi-tissue pannel from Slieker 2013. It includes Buccal, CD4T, CD8T, Mono, Bcell, NK, Gran.

Details

get_references returns the file with references data

Value

references dataset

Examples

get_references()

TestDataset

Description

get_TestDataset returns TestDataset

Usage

get_TestDataset()

Value

TestDataset dataset

Examples

get_TestDataset()