savR-package | Parse and analyze Illumina SAV files |
buildReports | Generate Illumina reports folder |
buildReports-method | Generate Illumina reports folder |
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 |
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 |
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 |
savExtractionFormat-class | Extraction Metrics formatter |
savFormat-class | Base class for formatters |
savProject-class | SAV project class |
savQualityFormat-class | Quality Metrics formatter |
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 |