Man pages for ploverso-pgdx/savR
Parse and analyze Illumina SAV files
| buildReports | Generate Illumina reports folder |
| clusterQualityGtN | Get the proportion of clusters over a specified quality... |
| 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 |
