Package 'methylclockData'

Title: Data for methylclock package
Description: Collection of 9 datasets, andrews and bakulski cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete, combined cord blood, cord bloo d gse68456, gervin and lyle cord blood, guintivano dlpfc and saliva gse48472". Data downloaded from [meffil](https://github.com/perishky/meffil/). Data used to estimate cell counts using Extrinsic epigenetic age acceleration (EEAA) method Collection of 12 datasets to use with MethylClock package to estimate chronological and gestational DNA methylationwith estimators to use wit different methylation clocks
Authors: Juan R. Gonzalez [aut], Dolors Pelegri-Siso [aut, cre]
Maintainer: Dolors Pelegri-Siso <[email protected]>
License: MIT + file LICENSE
Version: 1.20.0
Built: 2026-10-10 11:15:38 UTC
Source: https://github.com/bioc/methylclockData

Help Index

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()

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()

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()

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()

coefMayneGA

Description

get_coefMayneGA returns the Mayne's clock coefficients

Usage

get_coefMayneGA()

Value

coefMayneGA dataset

Examples

get_coefMayneGA()

coefPedBE

Description

get_coefPedBE returns the PedBE's clock coefficients

Usage

get_coefPedBE()

Value

coefPedBE dataset

Examples

get_coefPedBE()

coefSkin

Description

get_coefSkin returns the Horvath's skin+blood clock coefficients

Usage

get_coefSkin()

Value

coefSkin dataset

Examples

get_coefSkin()

coefTL

Description

get_coefTL returns the Telomere Length clock coefficients

Usage

get_coefTL()

Value

coefTL dataset

Examples

get_coefTL()

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()