qcReport {minfi} | R Documentation

## 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 aryee@jhu.edu.

### 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)

    }

[Package minfi version 1.34.0 Index]