minfi (version 1.18.2)

getQC: 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.

See Also

minfiQC for an all-in-one function.

Examples

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