# Parse and analyze Illumina SAV files

## Documentation for package ‘savR’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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