# rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers

## Documentation for package ‘rSFFreader’ version 0.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

rSFFreader-package | Base classes and methods for high-throughput sequence data stored in SFF files.
adapterClip | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
adapterClip-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
adapterClip<- | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
adapterClip<--method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
append-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
append-method | Class '"SffReadsQ"' for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent) and their quality scores
availableClipModes | availableClipModes
class:SffHeader | 'SffHeader'
class:SffReads | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
class:SffReadsQ | Class '"SffReadsQ"' for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent) and their quality scores
clipMode | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
clipMode-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
clipMode<- | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
clipMode<--method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
customClip | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
customClip-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
customClip<- | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
customClip<--method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
detail-method | 'SffHeader'
detail-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
detail-method | Class '"SffReadsQ"' for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent) and their quality scores
fullClip | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
fullClip-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
header | 'SffHeader'
header-method | 'SffHeader'
id-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
length-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
load454SampleData | Load the example 454 dataset
loadIonSampleData | Load the example Ion Torrent dataset
name-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
names-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
names<--method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
quality | Class '"SffReadsQ"' for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent) and their quality scores
quality-method | Class '"SffReadsQ"' for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent) and their quality scores
qualityClip | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
qualityClip-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
qualityClip<- | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
qualityClip<--method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
rawClip | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
rawClip-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
readSff | Read SFF-formatted files into SffReads or SffReadsQ objects
readSffGeometry | Read in basic statistics about an sff file
readSffHeader | Read in sff header
rSFFreader | Base classes and methods for high-throughput sequence data stored in SFF files.
SffHeader | 'SffHeader'
SffHeader-class | 'SffHeader'
SffReads | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
SffReads-class | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
SffReadsQ | Class '"SffReadsQ"' for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent) and their quality scores
SffReadsQ-class | Class '"SffReadsQ"' for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent) and their quality scores
show-method | 'SffHeader'
show-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
solveSffSEW | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
sread | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
width-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
writeFasta-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
writeFastaQual | Class '"SffReadsQ"' for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent) and their quality scores
writeFastaQual-method | Class '"SffReadsQ"' for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent) and their quality scores
writeFastq-method | Class '"SffReadsQ"' for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent) and their quality scores
writePhredQual | Class '"SffReadsQ"' for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent) and their quality scores
writePhredQual-method | Class '"SffReadsQ"' for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent) and their quality scores
[-method | Class '"SffReads"'. A class for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent)
[-method | Class '"SffReadsQ"' for next generation reads stored in SFF files (Roche 454 and Life Sciences Ion Torrent) and their quality scores