DNAmAge {methylclock}R Documentation

DNAm age estimation using different DNA methylation clocks.

Description

DNAm age estimation using different DNA methylation clocks.

Usage

DNAmAge(
    x,
    clocks = "all",
    toBetas = FALSE,
    fastImp = FALSE,
    normalize = FALSE,
    age,
    cell.count = TRUE,
    cell.count.reference = "blood gse35069 complete",
    min.perc = 0.8,
    ...
)

Arguments

x

data.frame (Individual in columns, CpGs in rows, CpG names in first colum - i.e. Horvath's format), matrix (individuals in columns and Cpgs in rows having CpG names in the rownames), ExpressionSet or GenomicRatioSet.

clocks

the methods used for estimating DNAmAge. Currrently "Horvath", "Hannum", "Levine", "BNN", "Horvath2", "PedBE" and "all" are available. Default is "all" and all clocks are estimated.

toBetas

Should data be transformed to beta values? Default is FALSE. If TRUE, it implies data are M values.

fastImp

Is fast imputation performed if necessary? (see details). Default is FALSE

normalize

Is Horvath's normalization performed? By default is FALSE

age

individual's chronological age.

cell.count

Are cell counts estimated? Default is TRUE.

cell.count.reference

Used when 'cell.count' is TRUE. Default is "blood gse35069 complete".See 'meffil::meffil.list.cell.count.references()' for possible values.

min.perc

Indicates the minimum conicidence percentage required between CpGs in or dataframee x and CpGs in clock coefficients to perform the calculation. If min.prec is too low, the estimated gestational DNAm age can be poor

...

Other arguments to be passed through impute package

Details

Imputation is performed when having missing data. Fast imputation is performed by ... what about imputing only when CpGs for the clock are missing?

Value

The estimated chronological and biological mDNA age

Examples

MethylationData <- get_MethylationDataExample()
age.example55 <- DNAmAge(MethylationData)

[Package methylclock version 1.0.1 Index]