savR: Parse and analyze Illumina SAV files

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

AuthorR. Brent Calder
Date of publicationNone
MaintainerR. Brent Calder <brent.calder@einstein.yu.edu>
LicenseAGPL-3
Version1.12.0
https://github.com/bcalder/savR

View on Bioconductor

Functions

buildReports Man page
buildReports,savProject,character-method Man page
buildReports,savProject,missing-method Man page
clusterQualityGtN Man page
clusterQualityGtN,savProject,integer,integer,integer Man page
clusterQualityGtN,savProject,integer,integer,integer-method Man page
clusters Man page
clusters,savProject,integer-method Man page
correctedIntensities Man page
correctedIntensities,savProject-method Man page
cycles Man page
cycles,savProject-method Man page
directions Man page
directions,savProject-method Man page
errorMetrics Man page
errorMetrics,savProject-method Man page
extractionMetrics Man page
extractionMetrics,savProject-method Man page
flowcellLayout Man page
flowcellLayout,savProject-method Man page
illuminaFlowCellLayout-class Man page
illuminaRead-class Man page
location Man page
location,savProject-method Man page
pfBoxplot Man page
pfBoxplot,savProject-method Man page
pfClusters Man page
pfClusters,savProject,integer Man page
pfClusters,savProject,integer-method Man page
plotFWHM Man page
plotFWHM,savProject,integer,character-method Man page
plotFWHM,savProject,integer,missing-method Man page
plotFWHM,savProject,missing,character-method Man page
plotFWHM,savProject,missing,missing-method Man page
plotIntensity Man page
plotIntensity,savProject,integer,character-method Man page
plotIntensity,savProject,integer,missing-method Man page
plotIntensity,savProject,missing,character-method Man page
plotIntensity,savProject,missing,missing-method Man page
plotQGT30 Man page
plotQGT30,savProject,integer-method Man page
plotQGT30,savProject,missing-method Man page
qualityHeatmap Man page
qualityHeatmap,savProject,integer,integer,logical-method Man page
qualityHeatmap,savProject,numeric,numeric,missing-method Man page
qualityMetrics Man page
qualityMetrics,savProject-method Man page
reads Man page
reads,savProject-method Man page
run Man page
run,savProject-method Man page
savCorrectedIntensityFormat-class Man page
savData-class Man page
savErrorFormat-class Man page
savExtractionFormat-class Man page
savFormat-class Man page
savProject-class Man page
savQualityFormat-class Man page
savQualityFormatV5-class Man page
savR Man page
savR,character-method Man page
savR,missing-method Man page
savR-package Man page
savTileFormat-class Man page
tileMetrics Man page
tileMetrics,savProject-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.