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savR

savR is an R package to parse Illumina Sequence Analysis Viewer (InterOp) files for downstream analysis.

Current release version 1.7.5.

Example

library(savR)
example(savR)

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Version

Version

1.10.0

License

AGPL-3

Issues

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Repository

https://github.com/bcalder/savR

Maintainer

R Brent Calder

Last Published

February 15th, 2017

Functions in savR (1.10.0)

illuminaFlowCellLayout-class

Layout of an Illumina flowcell

Parse and analyze Illumina SAV files

correctedIntensities

Get Corrected Intensity data

Generate Illumina reports folder

savQualityFormat-class

Quality Metrics formatter

Get Tile Metrics

Get number of clusters per lane

savExtractionFormat-class

Extraction Metrics formatter

Get flowcell layout

Get Flowcell folder location

Get the total number of cycles

savErrorFormat-class

Error Metrics formatter

extractionMetrics

Get Extraction Metrics

Plot flowcell intensity by base and cycle

savCorrectedIntensityFormat-class

Corrected Intensity formatter

Generate a heatmap of qualities

savTileFormat-class

Tile Metrics formatter

Structure for holding parsed InterOp headers and data

clusterQualityGtN

Get the proportion of clusters over a specified quality threshold

illuminaRead-class

savQualityFormatV5-class

Quality Metrics formatter version 5

savFormat-class

Base class for formatters

Build a SAV project

Plot Quality > 30 for a flowcell

savProject-class

SAV project class

Get Error Metrics

Get the number of sequence reads

Get Quality Metrics data

Generate FWHM plots

Get number of PF clusters per lane