methyAge: Methylation Age estimator

In xuz1/ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Methylation Age estimator

Description

To calculate Methylation Age using Hovath, Hannum or PhenoAge methods and pace of aging DunedinPACE.

Usage

methyAge(beta,fastImputation=FALSE,normalize=TRUE,nCores=2)

Arguments

beta	Methylation beta value matrix with CpG names(row names) and sample ids(column names).
fastImputation	If "TRUE" reference methylation values will used for imputation, if "FALSE", KNN nearest neighbor method will be used.
normalize	TRUE or FALSE, if TRUE, Hovath modified BMIQ method will be used to perform normalization.
nCores	Number of cores will be used for normalization

Value

A data frame with rows for sample and columns for types of methylation age.

Author(s)

Zongli Xu

References

Horvath S. DNA methylation age of human tissues and cell types. Genome biology 2013 14:R115.

Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, et al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Molecular cell 2013 49:359-367.

Levine ME, Lu AT, Quach A, Chen BH, Assimes TL, Bandinelli S, et al. An epigenetic biomarker of aging for lifespan and healthspan. Aging (Albany NY) 2018 10:573-591.

Daniel W Belsky, Avshalom Caspi, David L Corcoran,et al. DunedinPACE, a DNA methylation biomarker of the pace of aging. eLife, 2022

Examples

require(minfiData)
path <- file.path(find.package("minfiData"),"extdata")
#based on rgDataset
rgSet <- readidat(path = path,recursive = TRUE)
meth=getmeth(rgSet)
beta=getB(meth)
mage=methyAge(beta)

xuz1/ENmix documentation built on Nov. 24, 2024, 4:31 a.m.