/usr/lib/R/site-library/savR/INDEX is in r-bioc-savr 1.16.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | buildReports Generate Illumina reports folder
clusterQualityGtN Get the proportion of clusters over a specified
quality threshold
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
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