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

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

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.

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.

Value

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

Author(s)

Martin Aryee [e-mail].

See Also

mdsPlot, controlStripPlot, densityPlot, densityBeanPlot

Examples

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)

}

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