Parse and analyze Illumina SAV files


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Documentation for package ‘savR’ version 1.4.0

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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