getSex {minfi} | R Documentation

## Estimating sample sex based on methylation data

### Description

Estimates samples sex based on methylation data.

### Usage

    getSex(object = NULL, cutoff = -2)
    addSex(object, sex = NULL)
    plotSex(object, id = NULL)

### Arguments

`object` | An object of class `[Genomic]MethylSet`.
`cutoff` | What should the difference in log2 copynumber be between males and females.
`sex` | An optional character vector of sex (with values `M` and `F`).
`id` | Text used as plotting symbols in the `plotSex` function. Used for sample identification on the plot.

### Details

Estimation of sex is based on the median values of measurements on the X and Y chromosomes respectively. If `yMed` - `xMed` is less than `cutoff` we predict a female, otherwise male.

### Value

For `getSex`, a `DataFrame` with columns `predictedSex` (a character with values `M` and `F`), `xMed` and `yMed`, which are the chip-wide medians of measurements on the two sex chromosomes.

For `addSex`, an object of the same type as `object` but with the output of `getSex(object)` added to the pheno data.

For `plotSex`, a plot of `xMed` vs. `yMed`, which are the chip-wide medians of measurements on the two sex chromosomes, coloured by `predictedSex`.

### Author(s)

Rafael A. Irizarry, Kasper D. Hansen, Peter F. Hickey

### Examples

    if(require(minfiData)) {
      GMsetEx <- mapToGenome(MsetEx)
      estSex <- getSex(GMsetEx)
      GMsetEx <- addSex(GMsetEx, sex = estSex)
    }

[Package minfi version 1.38.0 Index]