minfiQC {minfi} | R Documentation

## easy one-step QC of methylation object

### Description

This function combines a number of functions into a simple to use, one step QC step/

### Usage

    minfiQC(object, fixOutliers = TRUE, verbose = FALSE)

### Arguments

`object` | An object of class `[Genomic]MethylSet`.
`fixOutliers` | Should the function fix outlying observations (using `fixMethOutliers`) before running QC?
`verbose` | Should the function be verbose?

### Details

A number of functions are run sequentially on the `object`.

First outlier values are thresholded using `fixMethOutliers`. Then qc is performed using `getQC` and then sample specific sex is estimated using `getSex`.

### Value

A list with two values,

`object` | The `object` processed by `fixMethOutliers` and with a column `predictedSex` added to the pheno data.
`qc` | A `DataFrame` with columns from the output of `getQC` and `getSex`

### Author(s)

Kasper D. Hansen

### See Also

`getSex`, `getQC`, `fixMethOutliers`

### Examples

    if(require(minfiData)) {
      out <- minfiQC(MsetEx)
      ## plotQC(out$qc)
      ## plotSex(out$sex)
    }

[Package minfi version 1.28.4 Index]