rSFFreader package - RDocumentation

rSFFreader

rSFFreader is a R package to read in and manipulate high throughput sequence data stored in the SFF file format. Currently Roche 454 sequencers and Life Sciences Ion Torrent sequencers output data in this format.

Specificiation are written such that they abide by the description http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=formats#sff

Future development will include

Writing out SFF files Reading in flowgrams Integration of flowgrams with sequence data

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Version

0.20.0

License

Artistic-2.0

Maintainer

Matt Settles

Last Published

February 15th, 2017

Functions in rSFFreader (0.20.0)

SffHeader-class

SffHeader

loadIonSampleData

Load the example Ion Torrent dataset

Class "SffReads". A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)

readSffGeometry

Read in basic statistics about an sff file

rSFFreader-package

Base classes and methods for high-throughput sequence data stored in SFF files.

SffReadsQ-class

Class "SffReadsQ" for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent) and their quality scores

rSFFreader internals

load454SampleData

Load the example 454 dataset

readSff

Read SFF-formatted files into SffReads or SffReadsQ objects