qcReport: QC report for Illumina Infinium Human Methylation 450k arrays
In minfi: Analyze Illumina Infinium DNA methylation arrays

Description Usage Arguments Details Value Author(s) See Also Examples

Produces a PDF QC report for Illumina Infinium Human Methylation 450k arrays, useful for identifying failed samples.

qcReport(rgSet, sampNames = NULL, sampGroups = NULL, pdf = "qcReport.pdf",
    maxSamplesPerPage = 24, controls = c("BISULFITE CONVERSION I",
    "BISULFITE CONVERSION II", "EXTENSION", "HYBRIDIZATION",
    "NON-POLYMORPHIC", "SPECIFICITY I", "SPECIFICITY II", "TARGET REMOVAL"))

`rgSet`	An object of class `RGChannelSet`.
`sampNames`	Sample names to be used for labels.
`sampGroups`	Sample groups to be used for labels.
`pdf`	Path and name of the PDF output file.
`maxSamplesPerPage`	Maximum number of samples to plot per page in those sections that plot each sample separately.
`controls`	The control probe types to include in the report.

This function produces a QC report as a PDF file. It is a useful first step after reading in a new dataset to get an overview of quality and to flag potentially problematic samples.

No return value. A PDF is produced as a side-effect.

Martin Aryee aryee@jhu.edu.

mdsPlot, controlStripPlot, densityPlot, densityBeanPlot

if (require(minfiData)) {

names <- pData(RGsetEx)$Sample_Name
groups <- pData(RGsetEx)$Sample_Group

## Not run: 
qcReport(RGsetEx, sampNames=names, sampGroups=groups, pdf="qcReport.pdf")

## End(Not run)

}