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


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Documentation for package ‘rSFFreader’ version 0.26.0

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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