rSFFreader: rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers
Version 0.24.0

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.

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AuthorMatt Settles <mattsettles@gmail.com>, Sam Hunter, Brice Sarver, Ilia Zhbannikov, Kyu-Chul Cho
Bioconductor views DataImport Sequencing
Date of publicationNone
MaintainerMatt Settles <mattsettles@gmail.com>
LicenseArtistic-2.0
Version0.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rSFFreader")

Man pages

availableClipModes: availableClipModes
load454SampleData: Load the example 454 dataset
loadIonSampleData: Load the example Ion Torrent dataset
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-internals: rSFFreader internals
rSFFreader-package: Base classes and methods for high-throughput sequence data...
SffHeader-class: 'SffHeader'
SffReads-class: Class '"SffReads"'. A class for next generation reads stored...
SffReadsQ-class: Class '"SffReadsQ"' for next generation reads stored in SFF...

Functions

.sffValidity Man page
.solveIRangeSEW Man page
SffHeader Man page
SffHeader-class Man page
SffReads Man page
SffReads-class Man page
SffReadsQ Man page Source code
SffReadsQ-class Man page
SffReadsQ_subset Source code
SffReads_subset Source code
[,SffReads,ANY,ANY-method Man page
[,SffReads,ANY,missing-method Man page
[,SffReads,missing,ANY-method Man page
[,SffReads,missing,missing-method Man page
[,SffReadsQ,ANY,ANY-method Man page
[,SffReadsQ,ANY,missing-method Man page
[,SffReadsQ,missing,ANY-method Man page
[,SffReadsQ,missing,missing-method Man page
adapterClip Man page
adapterClip,SffReads-method Man page
adapterClip<- Man page
adapterClip<-,SffReads-method Man page
append,SffReads,SffReads-method Man page
append,SffReadsQ,SffReadsQ-method Man page
availableClipModes Man page Source code
class:SffHeader Man page
class:SffReads Man page
class:SffReadsQ Man page
clipMode Man page
clipMode,SffReads-method Man page
clipMode<- Man page
clipMode<-,SffReads-method Man page
customClip Man page
customClip,SffReads-method Man page
customClip<- Man page
customClip<-,SffReads-method Man page
detail,SffHeader-method Man page
detail,SffReads-method Man page
detail,SffReadsQ-method Man page
fixSFFclipPoints2Iranges Source code
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 Source code
loadIonSampleData Man page Source code
name,SffReads-method Man page
names,SffReads-method Man page
names<-,SffReads,ANY-method Man page
quality Man page
quality,ANY-method Man page
qualityClip Man page
qualityClip,SffReads-method Man page
qualityClip<- Man page
qualityClip<-,SffReads-method Man page
rSFFreader Man page
rSFFreader-package Man page
rawClip Man page
rawClip,SffReads-method Man page
readSff Man page Source code
readSffGeometry Man page Source code
readSffHeader Man page Source code
sffValidity Source code
show,SffHeader-method Man page
show,SffReads-method Man page
solveIRangeSEW Source code
solveSffSEW Man page
sread Man page
sread,ANY-method Man page
width,SffReads-method Man page
writeFasta,SffReads-method Man page
writeFastaQual Man page
writeFastaQual,SffReadsQ-method Man page
writeFastq,SffReadsQ,ANY-method Man page
writePhredQual Man page
writePhredQual,FastqQuality-method Man page
writePhredQual,SffReadsQ-method Man page

Files

.BBSoptions
DESCRIPTION
NAMESPACE
NEWS
R
R/allClasses.R
R/allGenerics.R
R/methods-Misc.R
R/methods-SffHeader.R
R/methods-SffReads.R
R/methods-SffReadsQ.R
R/readSFF.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/rSFFreader.R
inst/doc/rSFFreader.Rnw
inst/doc/rSFFreader.pdf
inst/extdata
inst/extdata/Small454Test.sff
inst/extdata/SmallTorrentTest.sff
man
man/SffHeader-class.Rd
man/SffReads-class.Rd
man/SffReadsQ-class.Rd
man/availableClipModes.Rd
man/load454SampleData.Rd
man/loadIonSampleData.Rd
man/rSFFreader-internals.Rd
man/rSFFreader-package.Rd
man/readsff.Rd
man/readsffgeometry.Rd
man/readsffheader.Rd
src
src/Biostrings_stubs.c
src/IRanges_stubs.c
src/Makevars.win
src/R_init_rSFFreader.c
src/S4Vectors_stubs.c
src/SFF-io.c
src/XVector_stubs.c
src/rSFFreader.h
vignettes
vignettes/rSFFreader.Rnw
rSFFreader documentation built on May 20, 2017, 10:08 p.m.