minfi (version 1.18.2)

qcReport: QC report for Illumina Infinium Human Methylation 450k arrays

Description

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

Usage

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"))

Arguments

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.

Value

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

Details

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.

See Also

mdsPlot, controlStripPlot, densityPlot, densityBeanPlot

Examples

if (require(minfiData)) {

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

qcReport(RGsetEx, sampNames=names, sampGroups=groups, pdf="qcReport.pdf")

}