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

rSFFreader reads sequence, qualities and clip point values from sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers into similar classes as are present for fastq files.

AuthorMatt Settles <mattsettles@gmail.com>, Sam Hunter, Brice Sarver, Ilia Zhbannikov, Kyu-Chul Cho
Date of publicationNone
MaintainerMatt Settles <mattsettles@gmail.com>
LicenseArtistic-2.0
Version0.22.0

View on Bioconductor

Functions

adapterClip Man page
adapterClip<- Man page
adapterClip<-,SffReads-method Man page
adapterClip,SffReads-method Man page
append,SffReadsQ,SffReadsQ-method Man page
append,SffReads,SffReads-method Man page
availableClipModes Man page
class:SffHeader Man page
class:SffReads Man page
class:SffReadsQ Man page
clipMode Man page
clipMode<- Man page
clipMode<-,SffReads-method Man page
clipMode,SffReads-method Man page
customClip Man page
customClip<- Man page
customClip<-,SffReads-method Man page
customClip,SffReads-method Man page
detail,SffHeader-method Man page
detail,SffReads-method Man page
detail,SffReadsQ-method Man page
fullClip Man page
fullClip,SffReads-method Man page
header Man page
header,SffHeader-method Man page
id,SffReads-method Man page
length,SffReads-method Man page
load454SampleData Man page
loadIonSampleData Man page
name,SffReads-method Man page
names<-,SffReads,ANY-method Man page
names,SffReads-method Man page
quality Man page
quality,ANY-method Man page
qualityClip Man page
qualityClip<- Man page
qualityClip<-,SffReads-method Man page
qualityClip,SffReads-method Man page
rawClip Man page
rawClip,SffReads-method Man page
readSff Man page
readSffGeometry Man page
readSffHeader Man page
rSFFreader Man page
rSFFreader-package Man page
SffHeader Man page
SffHeader-class Man page
SffReads Man page
[,SffReads,ANY,ANY-method Man page
[,SffReads,ANY,missing-method Man page
SffReads-class Man page
[,SffReads,missing,ANY-method Man page
[,SffReads,missing,missing-method Man page
SffReadsQ Man page
[,SffReadsQ,ANY,ANY-method Man page
[,SffReadsQ,ANY,missing-method Man page
SffReadsQ-class Man page
[,SffReadsQ,missing,ANY-method Man page
[,SffReadsQ,missing,missing-method Man page
.sffValidity Man page
show,SffHeader-method Man page
show,SffReads-method Man page
.solveIRangeSEW Man page
solveSffSEW Man page
sread Man page
sread,ANY-method Man page
width,SffReads-method Man page
writeFastaQual Man page
writeFastaQual,SffReadsQ-method Man page
writeFasta,SffReads-method Man page
writeFastq,SffReadsQ,ANY-method Man page
writePhredQual Man page
writePhredQual,FastqQuality-method Man page
writePhredQual,SffReadsQ-method Man page

Files

rSFFreader/.BBSoptions
rSFFreader/DESCRIPTION
rSFFreader/NAMESPACE
rSFFreader/NEWS
rSFFreader/R
rSFFreader/R/allClasses.R rSFFreader/R/allGenerics.R rSFFreader/R/methods-Misc.R rSFFreader/R/methods-SffHeader.R rSFFreader/R/methods-SffReads.R rSFFreader/R/methods-SffReadsQ.R rSFFreader/R/readSFF.R
rSFFreader/README.md
rSFFreader/build
rSFFreader/build/vignette.rds
rSFFreader/inst
rSFFreader/inst/doc
rSFFreader/inst/doc/rSFFreader.R
rSFFreader/inst/doc/rSFFreader.Rnw
rSFFreader/inst/doc/rSFFreader.pdf
rSFFreader/inst/extdata
rSFFreader/inst/extdata/Small454Test.sff
rSFFreader/inst/extdata/SmallTorrentTest.sff
rSFFreader/man
rSFFreader/man/SffHeader-class.Rd rSFFreader/man/SffReads-class.Rd rSFFreader/man/SffReadsQ-class.Rd rSFFreader/man/availableClipModes.Rd rSFFreader/man/load454SampleData.Rd rSFFreader/man/loadIonSampleData.Rd rSFFreader/man/rSFFreader-internals.Rd rSFFreader/man/rSFFreader-package.Rd rSFFreader/man/readsff.Rd rSFFreader/man/readsffgeometry.Rd rSFFreader/man/readsffheader.Rd
rSFFreader/src
rSFFreader/src/Biostrings_stubs.c
rSFFreader/src/IRanges_stubs.c
rSFFreader/src/Makevars.win
rSFFreader/src/R_init_rSFFreader.c
rSFFreader/src/S4Vectors_stubs.c
rSFFreader/src/SFF-io.c
rSFFreader/src/XVector_stubs.c
rSFFreader/src/rSFFreader.h
rSFFreader/vignettes
rSFFreader/vignettes/rSFFreader.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.