DNAmGA {methylclock} | R Documentation

## Gestational DNAm age estimation using different DNA methylation clocks.

### Description

Gestational DNAm age estimation using different DNA methylation clocks.

### Usage

    DNAmGA(
        x,
        toBetas = FALSE,
        fastImp = FALSE,
        normalize = FALSE,
        age,
        cell.count = TRUE,
        cell.count.reference = "andrews and bakulski cord blood",
        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.
`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. Required to compute gestational age difference output
`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 gestational DNAm age

### Examples

    TestDataset <- get_TestDataset()
    TestDataset[1:5, ]
    ga.test <- DNAmGA(TestDataset)

[Package methylclock version 1.0.1 Index]