qcReport {minfi} | R Documentation |
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 |
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) }