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 |