oligo: Preprocessing tools for oligonucleotide arrays
Version 1.40.1

A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

Browse man pages Browse package API and functions Browse package files

AuthorBenilton Carvalho and Rafael Irizarry
Bioconductor views DataImport DifferentialExpression ExonArray GeneExpression Microarray OneChannel Preprocessing SNP TwoChannel
Date of publicationNone
MaintainerBenilton Carvalho <benilton@unicamp.br>
LicenseLGPL (>= 2)
Version1.40.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("oligo")

Man pages

basecontent: Sequence Base Contents
basicPLM: Simplified interface to PLM.
basicRMA: Simplified interface to RMA.
boxplot: Boxplot
chromosome: Accessor for chromosome information
colors: Create set of colors, interpolating through a set of...
coordinates: Accessors for physical array coordinates.
crlmm: Genotype Calls
fitProbeLevelModel: Tool to fit Probe Level Models.
getAffinitySplineCoefficients: Estimate affinity coefficients.
getBaseProfile: Compute and plot nucleotide profile.
getContainer: Get container information for NimbleGen Tiling Arrays.
getCrlmmSummaries: Function to get CRLMM summaries saved to disk
getNetAffx: NetAffx Biological Annotations
getNgsColorsInfo: Helper function to extract color information for filenames on...
getPlatformDesign: Retrieve Platform Design object
getProbeInfo: Probe information selector.
hist: Density estimate
image: Display a pseudo-image of a microarray chip
Index-methods: Accessors for PM, MM or background probes indices.
IntensityMatrix-methods: Accessors and replacement methods for the intensity/PM/MM/BG...
justSNPRMA: Summarization of SNP data
list.xysfiles: List XYS files
MAplot-methods: MA plots
oligoDefunct: Defunct Functions in Package 'oligo'
oligo-package: The oligo package: a tool for low-level analysis of...
oligoPLM-class: Class '"oligoPLM"'
paCalls: Methods for P/A Calls
plotM-methods: Methods for Log-Ratio plotting
pmAllele: Access the allele information for PM probes.
pmFragmentLength: Access the fragment length for PM probes.
pmPosition: Accessor to position information
pmStrand: Accessor to the strand information
preprocessTools: Tools for microarray preprocessing.
probeNames: Accessor to feature names
read.celfiles: Parser to CEL files
readSummaries: Read summaries generated by crlmm
read.xysfiles: Parser to XYS files
rma-methods: RMA - Robust Multichip Average algorithm
runDate: Date of scan
sequenceDesignMatrix: Create design matrix for sequences
Sequences-methods: Probe Sequeces
snprma: Preprocessing SNP Arrays

Functions

AffyDate2Posix Source code
GetAffyTimeDateAsString Source code
HuberAllRowsByGroup Source code
LLR2conf Source code
MAplot Man page
MAplot,ExpressionSet-method Man page
MAplot,FeatureSet-method Man page
MAplot,PLMset-method Man page
MAplot,TilingFeatureSet-method Man page
MAplot,matrix-method Man page
MAplot-methods Man page
NUSE Man page Source code
NUSE,oligoPLM-method Man page
NgsDate2Posix Source code
RLE Man page Source code
RLE,oligoPLM-method Man page
alleleSetFrom Source code
annotation,oligoPLM-method Man page
availProbeInfo Man page Source code
backgroundCorrect Man page
backgroundCorrect,FeatureSet-method Man page
backgroundCorrect,ff_matrix-method Man page
backgroundCorrect,matrix-method Man page
backgroundCorrect-methods Man page
backgroundCorrectionMethods Man page Source code
basecontent Man page Source code
basicAnnotatedDataFrame Source code
basicMedianPolishBO Source code
basicMvApairsPlot Source code
basicMvAplot Source code
basicPData Source code
basicPData2 Source code
basicPLM Man page Source code
basicPhData1 Source code
basicPhData2 Source code
basicRMA Man page Source code
basicRMAbo Source code
bg Man page
bg,FeatureSet-method Man page
bg,TilingFeatureSet-method Man page
bg<- Man page
bg<-,FeatureSet,ff_matrix-method Man page
bg<-,FeatureSet,matrix-method Man page
bg<-,TilingFeatureSet,array-method Man page
bgLESN Source code
bgMAS Source code
bgMASFS Source code
bgSequence Man page
bgSequence,DBPDInfo-method Man page
bgSequence,ExonFeatureSet-method Man page
bgSequence,FeatureSet-method Man page
bgSequence,GeneFeatureSet-method Man page
bgShift Source code
bgStretch Source code
bgindex Man page
bgindex,DBPDInfo-method Man page
bgindex,FeatureSet-method Man page
boxplot Man page
boxplot,ExpressionSet-method Man page
boxplot,FeatureSet-method Man page
boxplot,PLMset-method Man page
boxplot,oligoPLM-method Man page
boxplot-methods Man page
checkChipTypes Source code
checkValidFilenames Source code
chromosome Man page
chromosome<- Man page
chromosome<-,AnnotatedDataFrame,character-method Man page
cleanPlatformName Man page Source code
cloneFS Source code
coef,oligoPLM-method Man page
coefs Man page
coefs.probe Man page
coefs.probe,oligoPLM-method Man page
computeDABG Source code
computePSDABG Source code
constantNorm Source code
crlmm Man page Source code
crlmm.old Source code
crlmm2 Source code
darkColors Man page Source code
divColors Man page Source code
f Source code
ffSubset Source code
fitAffySnpMixture Source code
fitAffySnpMixture2 Source code
fitAffySnpMixture56 Source code
fitPLM Man page
fitProbeLevelModel Man page Source code
g Source code
gcCounts Source code
genotypeByChromosome Source code
genotypeOne Source code
geometry,oligoPLM-method Man page
getAffinitySplineCoefficients Man page Source code
getAffySnpCalls Source code
getAffySnpCalls56 Source code
getAffySnpConfidence Source code
getAffySnpConfidence56 Source code
getAffySnpDistance Source code
getAffySnpDistanceSingle Source code
getAffySnpDistanceSingle56 Source code
getAffySnpGenotypeRegionParams Source code
getAffySnpPriors Source code
getAllRowsSomeCols Source code
getBaseProfile Man page Source code
getCelChipType Source code
getChrXIndex Source code
getContainer Man page
getContainer,TilingFeatureSet-method Man page
getContainer-methods Man page
getCrlmmSummaries Man page Source code
getDefaultParsNormAdv Source code
getFSetInfo Source code
getFeatureInfo Source code
getFidMetaProbesetCore Source code
getFidMetaProbesetExtended Source code
getFidMetaProbesetFull Source code
getFidProbeset Source code
getFilenames Source code
getFragmentLength Source code
getFromListAsVector Source code
getGenotypeRegionParams Source code
getInitialAffySnpCalls Source code
getInitialAffySnpCalls2 Source code
getMPSInfo Source code
getNetAffx Man page
getNetAffx,ExpressionSet-method Man page
getNetAffx-methods Man page
getNgsColorsInfo Man page Source code
getPD Man page
getPlatformDesign Man page
getPlatformDesign,FeatureSet-method Man page
getProbeIndex Source code
getProbeInfo Man page Source code
getProbeTargets Source code
getProbeTypes Source code
getRefDABG Source code
getSnpFragmentLength Source code
getSnpLocInfo Source code
getSnpNames Source code
getSnpProbeInfo Source code
getSomeRowsAllCols Source code
getSomeRowsSomeCols Source code
getX Man page
getX,DBPDInfo-method Man page
getX,FeatureSet-method Man page
getX-methods Man page
getY Man page
getY,DBPDInfo-method Man page
getY,FeatureSet-method Man page
getY-methods Man page
hist Man page
hist,ExpressionSet-method Man page
hist,FeatureSet-method Man page
hist-methods Man page
image Man page
image,FeatureSet-method Man page
image,PLMset-method Man page
image,oligoPLM-method Man page
image-methods Man page
intensity Man page
intensity,FeatureSet-method Man page
intensity<- Man page
intensity<-,FeatureSet-method Man page
invariantsetNorm Source code
invariantsetV Source code
justCRLMM Man page Source code
justCRLMM2 Source code
justCRLMMv2 Source code
justCRLMMv3 Source code
justCRLMMv4 Source code
justSNPRMA Man page Source code
list.xysfiles Man page Source code
liteNormalization Source code
liteNormalization2 Source code
loessNorm Source code
loessNormV Source code
manufacturer,oligoPLM-method Man page
maplot Source code
matDensity Source code
method Man page
method,oligoPLM-method Man page
mm Man page
mm,FeatureSet-method Man page
mm,TilingFeatureSet-method Man page
mm<- Man page
mm<-,FeatureSet,ANY,ANY,ff_matrix-method Man page
mm<-,FeatureSet,ANY,ANY,matrix-method Man page
mm<-,TilingFeatureSet,ANY,ANY,array-method Man page
mmSequence Man page
mmSequence,AffySNPPDInfo-method Man page
mmSequence,DBPDInfo-method Man page
mmSequence,FeatureSet-method Man page
mmindex Man page
mmindex,DBPDInfo-method Man page
mmindex,FeatureSet-method Man page
msgOK Source code
my.abind Source code
ncol,oligoPLM-method Man page
normalizationMethods Man page Source code
normalize,FeatureSet-method Man page
normalize,ff_matrix-method Man page
normalize,matrix-method Man page
normalizeAdv Source code
normalizeOne Source code
normalizeToTarget Man page
normalizeToTarget,ff_matrix-method Man page
normalizeToTarget,matrix-method Man page
normalizeToTarget-methods Man page
nprobes Man page
nprobes,oligoPLM-method Man page
nprobesets Man page
nprobesets,oligoPLM-method Man page
oligo-defunct Man page
oligo-package Man page
oligoPLM Man page
oligoPLM-class Man page
oligoReadCels Source code
oligoReadXys Source code
onAttach Source code
onUnload Source code
opset2eset Man page
opset2eset,oligoPLM-method Man page
outputEqualizer Source code
paCalls Man page
paCalls,ExonFeatureSet-method Man page
paCalls,ExpressionFeatureSet-method Man page
paCalls,GeneFeatureSet-method Man page
paMAS5 Source code
pair2xys Source code
plm1Probeset Source code
plotM Man page Source code
plotM,SnpQSet,character-method Man page
plotM,SnpQSet,integer-method Man page
plotM,SnpQSet,numeric-method Man page
plotM,TilingQSet,missing-method Man page
plotM-methods Man page
pm Man page
pm,FeatureSet-method Man page
pm,GenericFeatureSet-method Man page
pm,TilingFeatureSet-method Man page
pm<- Man page
pm<-,FeatureSet,ANY,ANY,ff_matrix-method Man page
pm<-,FeatureSet,ANY,ANY,matrix-method Man page
pm<-,GenericFeatureSet,ANY,ANY,ff_matrix-method Man page
pm<-,GenericFeatureSet,ANY,ANY,matrix-method Man page
pm<-,TilingFeatureSet,ANY,ANY,array-method Man page
pmAllele Man page
pmAllele,AffySNPPDInfo-method Man page
pmAllele,SnpFeatureSet-method Man page
pmChr Man page
pmChr,ExonFeatureSet-method Man page
pmChr,FeatureSet-method Man page
pmChr,GeneFeatureSet-method Man page
pmFragmentLength Man page
pmFragmentLength,AffySNPPDInfo-method Man page
pmFragmentLength,SnpFeatureSet-method Man page
pmOffset Man page
pmOffset,AffySNPPDInfo-method Man page
pmPosition Man page
pmPosition,ExpressionPDInfo-method Man page
pmPosition,FeatureSet-method Man page
pmPosition,TilingFeatureSet-method Man page
pmPosition,TilingPDInfo-method Man page
pmSequence Man page
pmSequence,AffyGenePDInfo-method Man page
pmSequence,AffySNPPDInfo-method Man page
pmSequence,DBPDInfo-method Man page
pmSequence,ExonFeatureSet-method Man page
pmSequence,FeatureSet-method Man page
pmSequence,GeneFeatureSet-method Man page
pmSequence,stArrayDBPDInfo-method Man page
pmStrand Man page
pmStrand,AffySNPPDInfo-method Man page
pmStrand,TilingFeatureSet-method Man page
pmindex Man page
pmindex,DBPDInfo-method Man page
pmindex,FeatureSet-method Man page
pmindex,GenericFeatureSet-method Man page
pmindex,GenericPDInfo-method Man page
pmindex,stArrayDBPDInfo-method Man page
probeNames Man page
probeNames,DBPDInfo-method Man page
probeNames,ExonFeatureSet-method Man page
probeNames,FeatureSet-method Man page
probeNames,GeneFeatureSet-method Man page
probeNames,stArrayDBPDInfo-method Man page
probesetNames Man page
probesetNames,FeatureSet-method Man page
qnTargetStatsLDSnode Source code
qnToTargetLDSnode Source code
qsplineNorm Source code
quantileNormalizationLDSmaster Source code
read.celfiles Man page Source code
read.celfiles2 Man page Source code
read.mc.celfiles Source code
read.xysfiles Man page Source code
read.xysfiles2 Man page Source code
readCEL Source code
readChipTypesFromCels Source code
readSummaries Man page Source code
readXysMatrix Source code
readonexysfile Source code
readxysHeader Source code
replaceAffySnpParams Source code
replaceAffySnpParamsSingle Source code
resids Man page
residualSE Man page
residualSE,oligoPLM-method Man page
residuals,oligoPLM-method Man page
rma Man page
rma,ExonFeatureSet-method Man page
rma,ExpressionFeatureSet-method Man page
rma,GeneFeatureSet-method Man page
rma,GenericFeatureSet-method Man page
rma,HTAFeatureSet-method Man page
rma,SnpCnvFeatureSet-method Man page
rma-methods Man page
rmaBgCorrectLDSmaster Source code
rmaBgCorrectLDSnode Source code
rowEntropy Source code
rowIndepChiSqTest Source code
runDate Man page
runDate,FeatureSet-method Man page
runDate-methods Man page
runPLM Source code
runSummarize Source code
saveAppendMatrix Source code
se Man page
se,oligoPLM-method Man page
se.probe Man page
se.probe,oligoPLM-method Man page
seqColors Man page Source code
seqColors2 Man page Source code
sequenceDesignMatrix Man page Source code
show,oligoPLM-method Man page
smartReadCEL Source code
smartReadXYS Source code
snpGenderCall Source code
snprma Man page Source code
snprma2 Source code
sqsFrom Source code
sqsFrom.SnpCnv Source code
stArrayPmInfo Source code Source code
summarizationMethods Man page Source code
summarize Man page
summarize,ff_matrix-method Man page
summarize,matrix-method Man page
summarize-methods Man page
trigammaInverse Source code
txtMsg Source code
updateAffySnpParams Source code
updateAffySnpParamsSingle Source code
weights,oligoPLM-method Man page

Files

.Rinstignore
CHANGES
DESCRIPTION
NAMESPACE
R
R/AllGenerics.R
R/functions-crlmm.R
R/functions-snprma.R
R/justCRLMM.R
R/justSNPRMA.R
R/methods-DBPDInfo.R
R/methods-ExonFeatureSet.R
R/methods-ExpressionFeatureSet.R
R/methods-ExpressionSet.R
R/methods-FeatureSet.R
R/methods-GeneFeatureSet.R
R/methods-GenericArrays.R
R/methods-HtaFeatureSet.R
R/methods-LDS.R
R/methods-PLMset.R
R/methods-SnpCnvFeatureSet.R
R/methods-SnpFeatureSet.R
R/methods-TilingFeatureSet.R
R/methods-background.R
R/methods-genotype.R
R/methods-normalization.R
R/methods-snp6.R
R/methods-summarization.R
R/read.celfiles.R
R/read.xysfiles.R
R/todo-snp.R
R/utils-general.R
R/utils-selectors.R
R/zzz.R
README.md
TODO.org
build
build/vignette.rds
cleanup
cleanup.win
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/oug.Rnw
inst/doc/oug.pdf
inst/scripts
inst/scripts/FrameworkPreprocessing.bib
inst/scripts/getVersions.sh
inst/scripts/oligoVignette.bib
inst/scripts/oug.Rnw
inst/scripts/oug.pdf
inst/scripts/primer.Rnw
inst/scripts/primer.pdf
inst/unitTests
inst/unitTests/fids_ref0.rda
inst/unitTests/gen_rma_t0.R
inst/unitTests/gen_selector0.R
inst/unitTests/i0.rda
inst/unitTests/rma_ref0.rda
inst/unitTests/test_rma.R
inst/unitTests/test_selector.R
man
man/Index-methods.Rd
man/IntensityMatrix-methods.Rd
man/MAplot-methods.Rd
man/Sequences-methods.Rd
man/basecontent.Rd
man/basicPLM.Rd
man/basicRMA.Rd
man/boxplot.Rd
man/chromosome.Rd
man/colors.Rd
man/coordinates.Rd
man/crlmm.Rd
man/fitProbeLevelModel.Rd
man/getAffinitySplineCoefficients.Rd
man/getBaseProfile.Rd
man/getContainer.Rd
man/getCrlmmSummaries.Rd
man/getNetAffx.Rd
man/getNgsColorsInfo.Rd
man/getPlatformDesign.Rd
man/getProbeInfo.Rd
man/hist.Rd
man/image.Rd
man/justSNPRMA.Rd
man/list.xysfiles.Rd
man/oligo-package.Rd
man/oligoDefunct.Rd
man/oligoPLM-class.Rd
man/paCalls.Rd
man/plotM-methods.Rd
man/pmAllele.Rd
man/pmFragmentLength.Rd
man/pmPosition.Rd
man/pmStrand.Rd
man/preprocessTools.Rd
man/probeNames.Rd
man/read.celfiles.Rd
man/read.xysfiles.Rd
man/readSummaries.Rd
man/rma-methods.Rd
man/runDate.Rd
man/sequenceDesignMatrix.Rd
man/snprma.Rd
src
src/DABG.c
src/Makevars
src/Makevars.win
src/ParserGzXYS.c
src/ParserXYS.c
src/baseProfile.c
src/basecontent.c
src/chipbackground.c
src/mas5calls.c
src/rma2.c
src/rma_common.c
src/rma_common.h
src/trimmed.c
tests
tests/doRUnit.R
vignettes
vignettes/Makefile
vignettes/oug.Rnw
oligo documentation built on May 20, 2017, 9:44 p.m.