methyAge: Methylation Age estimator
In ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Description Usage Arguments Value Author(s) References Examples

To calculate Methylation Age using Hovath, Hannum or PhenoAge methods

1	methyAge(beta,type="all",fastImputation=FALSE,normalize=TRUE,nCores=2)

`beta`	Methylation beta value matrix with CpG names(row names) and sample ids(column names).
`type`	Which method will be used for methylation age calculation: "hovath", "hannum", "phenoAge" or "all"
`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

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

Zongli Xu

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.

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)