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<h1> Parse and analyze Illumina SAV files
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</div><h2>Documentation for package ‘savR’ version 1.16.0</h2>
<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
<li><a href="../doc/index.html">User guides, package vignettes and other documentation.</a></li>
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<h2>Help Pages</h2>
<table width="100%">
<tr><td style="width: 25%;"><a href="savR-package.html">savR-package</a></td>
<td>Parse and analyze Illumina SAV files</td></tr>
<tr><td style="width: 25%;"><a href="buildReports.html">buildReports</a></td>
<td>Generate Illumina reports folder</td></tr>
<tr><td style="width: 25%;"><a href="buildReports.html">buildReports-method</a></td>
<td>Generate Illumina reports folder</td></tr>
<tr><td style="width: 25%;"><a href="clusterQualityGtN.html">clusterQualityGtN</a></td>
<td>Get the proportion of clusters over a specified quality threshold</td></tr>
<tr><td style="width: 25%;"><a href="clusterQualityGtN.html">clusterQualityGtN,savProject,integer,integer,integer</a></td>
<td>Get the proportion of clusters over a specified quality threshold</td></tr>
<tr><td style="width: 25%;"><a href="clusterQualityGtN.html">clusterQualityGtN-method</a></td>
<td>Get the proportion of clusters over a specified quality threshold</td></tr>
<tr><td style="width: 25%;"><a href="clusters.html">clusters</a></td>
<td>Get number of clusters per lane</td></tr>
<tr><td style="width: 25%;"><a href="clusters.html">clusters-method</a></td>
<td>Get number of clusters per lane</td></tr>
<tr><td style="width: 25%;"><a href="correctedIntensities.html">correctedIntensities</a></td>
<td>Get Corrected Intensity data</td></tr>
<tr><td style="width: 25%;"><a href="correctedIntensities.html">correctedIntensities-method</a></td>
<td>Get Corrected Intensity data</td></tr>
<tr><td style="width: 25%;"><a href="cycles.html">cycles</a></td>
<td>Get the total number of cycles</td></tr>
<tr><td style="width: 25%;"><a href="cycles.html">cycles-method</a></td>
<td>Get the total number of cycles</td></tr>
<tr><td style="width: 25%;"><a href="directions.html">directions</a></td>
<td>Get the number of sequence reads</td></tr>
<tr><td style="width: 25%;"><a href="directions.html">directions-method</a></td>
<td>Get the number of sequence reads</td></tr>
<tr><td style="width: 25%;"><a href="errorMetrics.html">errorMetrics</a></td>
<td>Get Error Metrics</td></tr>
<tr><td style="width: 25%;"><a href="errorMetrics.html">errorMetrics-method</a></td>
<td>Get Error Metrics</td></tr>
<tr><td style="width: 25%;"><a href="extractionMetrics.html">extractionMetrics</a></td>
<td>Get Extraction Metrics</td></tr>
<tr><td style="width: 25%;"><a href="extractionMetrics.html">extractionMetrics-method</a></td>
<td>Get Extraction Metrics</td></tr>
<tr><td style="width: 25%;"><a href="flowcellLayout.html">flowcellLayout</a></td>
<td>Get flowcell layout</td></tr>
<tr><td style="width: 25%;"><a href="flowcellLayout.html">flowcellLayout-method</a></td>
<td>Get flowcell layout</td></tr>
<tr><td style="width: 25%;"><a href="illuminaFlowCellLayout-class.html">illuminaFlowCellLayout-class</a></td>
<td>Layout of an Illumina flowcell</td></tr>
<tr><td style="width: 25%;"><a href="illuminaRead-class.html">illuminaRead-class</a></td>
<td>Illumina read</td></tr>
<tr><td style="width: 25%;"><a href="location.html">location</a></td>
<td>Get Flowcell folder location</td></tr>
<tr><td style="width: 25%;"><a href="location.html">location-method</a></td>
<td>Get Flowcell folder location</td></tr>
<tr><td style="width: 25%;"><a href="pfBoxplot.html">pfBoxplot</a></td>
<td>PF Boxplot</td></tr>
<tr><td style="width: 25%;"><a href="pfBoxplot.html">pfBoxplot-method</a></td>
<td>PF Boxplot</td></tr>
<tr><td style="width: 25%;"><a href="pfClusters.html">pfClusters</a></td>
<td>Get number of PF clusters per lane</td></tr>
<tr><td style="width: 25%;"><a href="pfClusters.html">pfClusters,savProject,integer</a></td>
<td>Get number of PF clusters per lane</td></tr>
<tr><td style="width: 25%;"><a href="pfClusters.html">pfClusters-method</a></td>
<td>Get number of PF clusters per lane</td></tr>
<tr><td style="width: 25%;"><a href="plotFWHM.html">plotFWHM</a></td>
<td>Generate FWHM plots</td></tr>
<tr><td style="width: 25%;"><a href="plotFWHM.html">plotFWHM-method</a></td>
<td>Generate FWHM plots</td></tr>
<tr><td style="width: 25%;"><a href="plotIntensity.html">plotIntensity</a></td>
<td>Plot flowcell intensity by base and cycle</td></tr>
<tr><td style="width: 25%;"><a href="plotIntensity.html">plotIntensity-method</a></td>
<td>Plot flowcell intensity by base and cycle</td></tr>
<tr><td style="width: 25%;"><a href="plotQGT30.html">plotQGT30</a></td>
<td>Plot Quality > 30 for a flowcell</td></tr>
<tr><td style="width: 25%;"><a href="plotQGT30.html">plotQGT30-method</a></td>
<td>Plot Quality > 30 for a flowcell</td></tr>
<tr><td style="width: 25%;"><a href="qualityHeatmap.html">qualityHeatmap</a></td>
<td>Generate a heatmap of qualities</td></tr>
<tr><td style="width: 25%;"><a href="qualityHeatmap.html">qualityHeatmap-method</a></td>
<td>Generate a heatmap of qualities</td></tr>
<tr><td style="width: 25%;"><a href="qualityMetrics.html">qualityMetrics</a></td>
<td>Get Quality Metrics data</td></tr>
<tr><td style="width: 25%;"><a href="qualityMetrics.html">qualityMetrics-method</a></td>
<td>Get Quality Metrics data</td></tr>
<tr><td style="width: 25%;"><a href="reads.html">reads</a></td>
<td>Get reads</td></tr>
<tr><td style="width: 25%;"><a href="reads.html">reads-method</a></td>
<td>Get reads</td></tr>
<tr><td style="width: 25%;"><a href="run.html">run</a></td>
<td>Get the Run ID</td></tr>
<tr><td style="width: 25%;"><a href="run.html">run-method</a></td>
<td>Get the Run ID</td></tr>
<tr><td style="width: 25%;"><a href="savCorrectedIntensityFormat-class.html">savCorrectedIntensityFormat-class</a></td>
<td>Corrected Intensity formatter</td></tr>
<tr><td style="width: 25%;"><a href="savData-class.html">savData-class</a></td>
<td>Structure for holding parsed InterOp headers and data</td></tr>
<tr><td style="width: 25%;"><a href="savErrorFormat-class.html">savErrorFormat-class</a></td>
<td>Error Metrics formatter</td></tr>
<tr><td style="width: 25%;"><a href="savExtractionFormat-class.html">savExtractionFormat-class</a></td>
<td>Extraction Metrics formatter</td></tr>
<tr><td style="width: 25%;"><a href="savFormat-class.html">savFormat-class</a></td>
<td>Base class for formatters</td></tr>
<tr><td style="width: 25%;"><a href="savProject-class.html">savProject-class</a></td>
<td>SAV project class</td></tr>
<tr><td style="width: 25%;"><a href="savQualityFormat-class.html">savQualityFormat-class</a></td>
<td>Quality Metrics formatter</td></tr>
<tr><td style="width: 25%;"><a href="savQualityFormatV5-class.html">savQualityFormatV5-class</a></td>
<td>Quality Metrics formatter version 5</td></tr>
<tr><td style="width: 25%;"><a href="savR.html">savR</a></td>
<td>Build a SAV project</td></tr>
<tr><td style="width: 25%;"><a href="savR.html">savR-method</a></td>
<td>Build a SAV project</td></tr>
<tr><td style="width: 25%;"><a href="savTileFormat-class.html">savTileFormat-class</a></td>
<td>Tile Metrics formatter</td></tr>
<tr><td style="width: 25%;"><a href="tileMetrics.html">tileMetrics</a></td>
<td>Get Tile Metrics</td></tr>
<tr><td style="width: 25%;"><a href="tileMetrics.html">tileMetrics-method</a></td>
<td>Get Tile Metrics</td></tr>
</table>
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