methyAge {ENmix} | R Documentation

## Calculate Methylation Age

### Description

Calculation of Methylation Age using Hovath, Hannum or PhenoAge methods

### Usage

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

### Arguments

`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

### Value

A data frame with sample ids and estimates 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.

### Examples

    ## Not run:
    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)

    ## End(Not run)

[Package ENmix version 1.23.5 Index]