| 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 |