buildReports            Generate Illumina reports folder
clusterQualityGtN       Get the proportion of clusters over a specified
                        quality threshold
clusters                Get number of clusters per lane
correctedIntensities    Get Corrected Intensity data
cycles                  Get the total number of cycles
directions              Get the number of sequence reads
errorMetrics            Get Error Metrics
extractionMetrics       Get Extraction Metrics
flowcellLayout          Get flowcell layout
illuminaFlowCellLayout-class
                        Layout of an Illumina flowcell
illuminaRead-class      Illumina read
location                Get Flowcell folder location
pfBoxplot               PF Boxplot
pfClusters              Get number of PF clusters per lane
plotFWHM                Generate FWHM plots
plotIntensity           Plot flowcell intensity by base and cycle
plotQGT30               Plot Quality > 30 for a flowcell
qualityHeatmap          Generate a heatmap of qualities
qualityMetrics          Get Quality Metrics data
reads                   Get reads
run                     Get the Run ID
savCorrectedIntensityFormat-class
                        Corrected Intensity formatter
savData-class           Structure for holding parsed InterOp headers
                        and data
savErrorFormat-class    Error Metrics formatter
savExtractionFormat-class
                        Extraction Metrics formatter
savFormat-class         Base class for formatters
savProject-class        SAV project class
savQualityFormat-class
                        Quality Metrics formatter
savQualityFormatV5-class
                        Quality Metrics formatter version 5
savR                    Build a SAV project
savR-package            Parse and analyze Illumina SAV files
savTileFormat-class     Tile Metrics formatter
tileMetrics             Get Tile Metrics
