Parse and analyze Illumina SAV files


[Up] [Top]

Documentation for package ‘savR’ version 1.34.0

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