savR: Parse and analyze Illumina SAV files
Version 1.14.0

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

AuthorR. Brent Calder
Bioconductor views Sequencing
Date of publicationNone
MaintainerR. Brent Calder <brent.calder@einstein.yu.edu>
LicenseAGPL-3
Version1.14.0
URL https://github.com/bcalder/savR
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("savR")

Getting started

Package overview
README.md

Popular man pages

buildReports: Generate Illumina reports folder
illuminaFlowCellLayout-class: Layout of an Illumina flowcell
location: Get Flowcell folder location
plotIntensity: Plot flowcell intensity by base and cycle
plotQGT30: Plot Quality > 30 for a flowcell
savFormat-class: Base class for formatters
savR: Build a SAV project
See all...

All man pages Function index File listing

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

Functions

addPosition Source code
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
getFlowcellStats Source code
getFormatQGT30 Source code
getInterOpFilePath Source code
illuminaFlowCellLayout-class Man page
illuminaRead-class Man page
init Source code
location Man page
location,savProject-method Man page
parseBin Source code
parseBinData Source code
parsesavQualityFormatV5 Source code
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
qFormat Source code
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
readToCycles Source code
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
subsetSide Source code
testVersion Source code
tileMetrics Man page
tileMetrics,savProject-method Man page

Files

CHANGES
DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/SavR-accessors.R
R/savR-methods.R
R/savR-package.R
R/show-methods.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/savR.R
inst/doc/savR.Rnw
inst/doc/savR.pdf
inst/extdata
inst/extdata/MiSeq
inst/extdata/MiSeq/InterOp
inst/extdata/MiSeq/InterOp/CorrectedIntMetricsOut.bin
inst/extdata/MiSeq/InterOp/ExtractionMetricsOut.bin
inst/extdata/MiSeq/InterOp/QMetricsOut.bin
inst/extdata/MiSeq/InterOp/TileMetricsOut.bin
inst/extdata/MiSeq/RunInfo.xml
man
man/buildReports.Rd
man/clusterQualityGtN.Rd
man/clusters.Rd
man/correctedIntensities.Rd
man/cycles.Rd
man/directions.Rd
man/errorMetrics.Rd
man/extractionMetrics.Rd
man/flowcellLayout.Rd
man/illuminaFlowCellLayout-class.Rd
man/illuminaRead-class.Rd
man/location.Rd
man/pfBoxplot.Rd
man/pfClusters.Rd
man/plotFWHM.Rd
man/plotIntensity.Rd
man/plotQGT30.Rd
man/qualityHeatmap.Rd
man/qualityMetrics.Rd
man/reads.Rd
man/run.Rd
man/savCorrectedIntensityFormat-class.Rd
man/savData-class.Rd
man/savErrorFormat-class.Rd
man/savExtractionFormat-class.Rd
man/savFormat-class.Rd
man/savProject-class.Rd
man/savQualityFormat-class.Rd
man/savQualityFormatV5-class.Rd
man/savR-package.Rd
man/savR.Rd
man/savTileFormat-class.Rd
man/tileMetrics.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_accessors.R
tests/testthat/test_load.R
vignettes
vignettes/savR.Rnw
savR documentation built on May 20, 2017, 10:40 p.m.

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