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

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

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)
}

hansenlab/minfi documentation built on Feb. 2, 2024, 11:23 a.m.