savR: Parse and analyze Illumina SAV files

Parse Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots.

Author
R. Brent Calder
Date of publication
None
Maintainer
R. Brent Calder <brent.calder@einstein.yu.edu>
License
AGPL-3
Version
1.12.0
URLs

View on Bioconductor

Man pages

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

Files in this package

savR/CHANGES
savR/DESCRIPTION
savR/NAMESPACE
savR/R
savR/R/AllClasses.R
savR/R/AllGenerics.R
savR/R/SavR-accessors.R
savR/R/savR-methods.R
savR/R/savR-package.R
savR/R/show-methods.R
savR/README.md
savR/build
savR/build/vignette.rds
savR/inst
savR/inst/doc
savR/inst/doc/savR.R
savR/inst/doc/savR.Rnw
savR/inst/doc/savR.pdf
savR/inst/extdata
savR/inst/extdata/MiSeq
savR/inst/extdata/MiSeq/InterOp
savR/inst/extdata/MiSeq/InterOp/CorrectedIntMetricsOut.bin
savR/inst/extdata/MiSeq/InterOp/ExtractionMetricsOut.bin
savR/inst/extdata/MiSeq/InterOp/QMetricsOut.bin
savR/inst/extdata/MiSeq/InterOp/TileMetricsOut.bin
savR/inst/extdata/MiSeq/RunInfo.xml
savR/man
savR/man/buildReports.Rd
savR/man/clusterQualityGtN.Rd
savR/man/clusters.Rd
savR/man/correctedIntensities.Rd
savR/man/cycles.Rd
savR/man/directions.Rd
savR/man/errorMetrics.Rd
savR/man/extractionMetrics.Rd
savR/man/flowcellLayout.Rd
savR/man/illuminaFlowCellLayout-class.Rd
savR/man/illuminaRead-class.Rd
savR/man/location.Rd
savR/man/pfBoxplot.Rd
savR/man/pfClusters.Rd
savR/man/plotFWHM.Rd
savR/man/plotIntensity.Rd
savR/man/plotQGT30.Rd
savR/man/qualityHeatmap.Rd
savR/man/qualityMetrics.Rd
savR/man/reads.Rd
savR/man/run.Rd
savR/man/savCorrectedIntensityFormat-class.Rd
savR/man/savData-class.Rd
savR/man/savErrorFormat-class.Rd
savR/man/savExtractionFormat-class.Rd
savR/man/savFormat-class.Rd
savR/man/savProject-class.Rd
savR/man/savQualityFormat-class.Rd
savR/man/savQualityFormatV5-class.Rd
savR/man/savR-package.Rd
savR/man/savR.Rd
savR/man/savTileFormat-class.Rd
savR/man/tileMetrics.Rd
savR/tests
savR/tests/testthat
savR/tests/testthat.R
savR/tests/testthat/test_accessors.R
savR/tests/testthat/test_load.R
savR/vignettes
savR/vignettes/savR.Rnw