getQC {minfi} | R Documentation

## Estimate sample-specific quality control (QC) for methylation data

### Description

Estimate sample-specific quality control (QC) for methylation data.

### Usage

    getQC(object)
    addQC(object, qc)
    plotQC(qc, badSampleCutoff = 10.5)

### Arguments

`object` | An object of class `[Genomic]MethylSet`.
`qc` | An object as produced by `getQC`.
`badSampleCutoff` | The cutoff for identifying a bad sample.

### Value

For `getQC`, a `DataFrame` with two columns: `mMed` and `uMed` which are the chipwide medians of the Meth and Unmeth channels.

For `addQC`, essentially `object` supplied to the function, but with two new columns added to the pheno data slot: `uMed` and `mMed`.

### Author(s)

Rafael A. Irizarry and Kasper D. Hansen

### See Also

`minfiQC` for an all-in-one function.

### Examples

    if(require(minfiData)){
      qc <- getQC(MsetEx)
      MsetEx <- addQC(MsetEx, qc = qc)
      ## plotQC(qc)
    }

[Package minfi version 1.38.0 Index]