Man pages for bcalder/savR
Parse and analyze Illumina SAV files

buildReportsGenerate Illumina reports folder
clusterQualityGtNGet the proportion of clusters over a specified quality...
clustersGet number of clusters per lane
correctedIntensitiesGet Corrected Intensity data
cyclesGet the total number of cycles
directionsGet the number of sequence reads
errorMetricsGet Error Metrics
extractionMetricsGet Extraction Metrics
flowcellLayoutGet flowcell layout
illuminaFlowCellLayout-classLayout of an Illumina flowcell
illuminaRead-classIllumina read
locationGet Flowcell folder location
pfBoxplotPF Boxplot
pfClustersGet number of PF clusters per lane
plotFWHMGenerate FWHM plots
plotIntensityPlot flowcell intensity by base and cycle
plotQGT30Plot Quality > 30 for a flowcell
qualityHeatmapGenerate a heatmap of qualities
qualityMetricsGet Quality Metrics data
readsGet reads
runGet the Run ID
savCorrectedIntensityFormat-classCorrected Intensity formatter
savData-classStructure for holding parsed InterOp headers and data
savErrorFormat-classError Metrics formatter
savExtractionFormat-classExtraction Metrics formatter
savFormat-classBase class for formatters
savParser-classIndex Metrics formatter
savProject-classSAV project class
savQualityFormat-classQuality Metrics formatter
savQualityFormatV5-classQuality Metrics formatter version 5
savQualityFormatV6-classQuality Metrics formatter version 6
savRBuild a SAV project
savR-packageParse and analyze Illumina SAV files
savTileFormat-classTile Metrics formatter
tileMetricsGet Tile Metrics
bcalder/savR documentation built on June 4, 2017, 3:13 a.m.