oligo: Preprocessing tools for oligonucleotide arrays

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

AuthorBenilton Carvalho and Rafael Irizarry
Date of publicationNone
MaintainerBenilton Carvalho <benilton@unicamp.br>
LicenseLGPL (>= 2)
Version1.38.0

View on Bioconductor

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

annotation,oligoPLM-method Man page
availProbeInfo Man page
backgroundCorrect Man page
backgroundCorrect,FeatureSet-method Man page
backgroundCorrect,ff_matrix-method Man page
backgroundCorrectionMethods Man page
backgroundCorrect,matrix-method Man page
backgroundCorrect-methods Man page
basecontent Man page
basicPLM Man page
basicRMA Man page
bg Man page
bg<- Man page
bg<-,FeatureSet,ff_matrix-method Man page
bg<-,FeatureSet,matrix-method Man page
bg,FeatureSet-method Man page
bgindex Man page
bgindex,DBPDInfo-method Man page
bgindex,FeatureSet-method Man page
bgSequence Man page
bgSequence,DBPDInfo-method Man page
bgSequence,ExonFeatureSet-method Man page
bgSequence,FeatureSet-method Man page
bgSequence,GeneFeatureSet-method Man page
bg<-,TilingFeatureSet,array-method Man page
bg,TilingFeatureSet-method Man page
boxplot Man page
boxplot,ExpressionSet-method Man page
boxplot,FeatureSet-method Man page
boxplot-methods Man page
boxplot,oligoPLM-method Man page
boxplot,PLMset-method Man page
chromosome Man page
chromosome<- Man page
chromosome<-,AnnotatedDataFrame,character-method Man page
cleanPlatformName Man page
coef,oligoPLM-method Man page
coefs Man page
coefs.probe Man page
coefs.probe,oligoPLM-method Man page
crlmm Man page
darkColors Man page
divColors Man page
fitPLM Man page
fitProbeLevelModel Man page
geometry,oligoPLM-method Man page
getAffinitySplineCoefficients Man page
getBaseProfile Man page
getContainer Man page
getContainer-methods Man page
getContainer,TilingFeatureSet-method Man page
getCrlmmSummaries Man page
getNetAffx Man page
getNetAffx,ExpressionSet-method Man page
getNetAffx-methods Man page
getNgsColorsInfo Man page
getPD Man page
getPlatformDesign Man page
getPlatformDesign,FeatureSet-method Man page
getProbeInfo Man page
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-methods Man page
image,oligoPLM-method Man page
image,PLMset-method Man page
intensity Man page
intensity<- Man page
intensity<-,FeatureSet-method Man page
intensity,FeatureSet-method Man page
justCRLMM Man page
justSNPRMA Man page
list.xysfiles Man page
manufacturer,oligoPLM-method Man page
MAplot Man page
MAplot,ExpressionSet-method Man page
MAplot,FeatureSet-method Man page
MAplot,matrix-method Man page
MAplot-methods Man page
MAplot,PLMset-method Man page
MAplot,TilingFeatureSet-method Man page
method Man page
method,oligoPLM-method Man page
mm Man page
mm<- Man page
mm<-,FeatureSet,ANY,ANY,ff_matrix-method Man page
mm<-,FeatureSet,ANY,ANY,matrix-method Man page
mm,FeatureSet-method Man page
mmindex Man page
mmindex,DBPDInfo-method Man page
mmindex,FeatureSet-method Man page
mmSequence Man page
mmSequence,AffySNPPDInfo-method Man page
mmSequence,DBPDInfo-method Man page
mmSequence,FeatureSet-method Man page
mm<-,TilingFeatureSet,ANY,ANY,array-method Man page
mm,TilingFeatureSet-method Man page
ncol,oligoPLM-method Man page
normalizationMethods Man page
normalize,FeatureSet-method Man page
normalize,ff_matrix-method Man page
normalize,matrix-method Man page
normalizeToTarget Man page
normalizeToTarget,ff_matrix-method Man page
normalizeToTarget,matrix-method Man page
normalizeToTarget-methods Man page
nprobes Man page
nprobesets Man page
nprobesets,oligoPLM-method Man page
nprobes,oligoPLM-method Man page
NUSE Man page
NUSE,oligoPLM-method Man page
oligo-defunct Man page
oligo-package Man page
oligoPLM Man page
oligoPLM-class Man page
paCalls Man page
paCalls,ExonFeatureSet-method Man page
paCalls,ExpressionFeatureSet-method Man page
paCalls,GeneFeatureSet-method Man page
plotM Man page
plotM-methods Man page
plotM,SnpQSet,character-method Man page
plotM,SnpQSet,integer-method Man page
plotM,SnpQSet,numeric-method Man page
plotM,TilingQSet,missing-method Man page
pm Man page
pm<- 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
pm<-,FeatureSet,ANY,ANY,ff_matrix-method Man page
pm<-,FeatureSet,ANY,ANY,matrix-method Man page
pm,FeatureSet-method Man page
pmFragmentLength Man page
pmFragmentLength,AffySNPPDInfo-method Man page
pmFragmentLength,SnpFeatureSet-method Man page
pm<-,GenericFeatureSet,ANY,ANY,ff_matrix-method Man page
pm<-,GenericFeatureSet,ANY,ANY,matrix-method Man page
pm,GenericFeatureSet-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
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
pm<-,TilingFeatureSet,ANY,ANY,array-method Man page
pm,TilingFeatureSet-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
read.celfiles Man page
read.celfiles2 Man page
readSummaries Man page
read.xysfiles Man page
read.xysfiles2 Man page
resids Man page
residualSE Man page
residualSE,oligoPLM-method Man page
residuals,oligoPLM-method Man page
RLE Man page
RLE,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-methods Man page
rma,SnpCnvFeatureSet-method Man page
runDate Man page
runDate,FeatureSet-method Man page
runDate-methods Man page
se Man page
se,oligoPLM-method Man page
se.probe Man page
se.probe,oligoPLM-method Man page
seqColors Man page
seqColors2 Man page
sequenceDesignMatrix Man page
show,oligoPLM-method Man page
snprma Man page
summarizationMethods Man page
summarize Man page
summarize,ff_matrix-method Man page
summarize,matrix-method Man page
summarize-methods Man page
weights,oligoPLM-method Man page

Files

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

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