Package: oligo 1.71.0
Benilton Carvalho
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).
Authors:
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oligo.pdf |oligo.html✨
oligo/json (API)
NEWS
| # Install 'oligo' in R: |
| install.packages('oligo', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/benilton/oligo/issues
On BioConductor:oligo-1.69.2(bioc 3.20)oligo-1.68.2(bioc 3.19)
microarrayonechanneltwochannelpreprocessingsnpdifferentialexpressionexonarraygeneexpressiondataimport
Last updated 17 days agofrom:b720ab9af6. Checks:OK: 1 ERROR: 1 WARNING: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.5-linux-x86_64 | ERROR | Oct 31 2024 |
| R-4.4-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-aarch64 | WARNING | Oct 31 2024 |
| R-4.3-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-aarch64 | WARNING | Oct 31 2024 |
Exports:annotationavailProbeInfobackgroundCorrectbackgroundCorrectionMethodsbasecontentbasicPLMbasicRMAbgbg<-bgSequenceboxplotcleanPlatformNamecoefcoefs.probecrlmmdarkColorsdbdivColorsexprsexprs<-fitProbeLevelModelgeometrygetAffinitySplineCoefficientsgetBaseProfilegetContainergetCrlmmSummariesgetNetAffxgetNgsColorsInfogetPDgetPlatformDesigngetProbeInfogetXgetYhistimageintensityjustCRLMMjustSNPRMAlist.xysfilesmanufacturerMAplotmethodmmmm<-mmindexmmSequencencolnormalizationMethodsnormalizenormalizeToTargetnprobesnprobesetsNUSEopset2esetpaCallsplotMpmpm<-pmAllelepmChrpmFragmentLengthpmindexpmOffsetpmPositionpmSequencepmStrandprobeNamesprobesetNamesread.celfilesread.celfiles2read.xysfilesread.xysfiles2readSummariesresidualsresidualSERLErmarunDatesese.probeseqColorsseqColors2sequenceDesignMatrixshowsnprmasummarizationMethodssummarizeweights
Dependencies:abindaffxparseraffyioaskpassBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapffforeachGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesiteratorsjsonlitelatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeoligoClassesopensslpkgconfigplogrpreprocessCoreR6rlangRSQLiteS4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsvctrsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The oligo package: a tool for low-level analysis of oligonucleotide arrays | oligo-package |
| Sequence Base Contents | basecontent |
| Simplified interface to PLM. | basicPLM |
| Simplified interface to RMA. | basicRMA |
| Boxplot | boxplot boxplot,ExpressionSet-method boxplot,FeatureSet-method boxplot,PLMset-method boxplot-methods |
| Accessor for chromosome information | chromosome chromosome<- chromosome<-,AnnotatedDataFrame,character-method pmChr pmChr,ExonFeatureSet-method pmChr,FeatureSet-method pmChr,GeneFeatureSet-method |
| Genotype Calls | crlmm justCRLMM |
| Create set of colors, interpolating through a set of preferred colors. | darkColors divColors seqColors seqColors2 |
| Tool to fit Probe Level Models. | fitProbeLevelModel |
| Estimate affinity coefficients. | getAffinitySplineCoefficients |
| Compute and plot nucleotide profile. | getBaseProfile |
| Get container information for NimbleGen Tiling Arrays. | getContainer getContainer,TilingFeatureSet-method getContainer-methods |
| Function to get CRLMM summaries saved to disk | getCrlmmSummaries |
| NetAffx Biological Annotations | getNetAffx getNetAffx,ExpressionSet-method getNetAffx-methods |
| Helper function to extract color information for filenames on NimbleGen arrays. | getNgsColorsInfo |
| Retrieve Platform Design object | getPD getPlatformDesign getPlatformDesign,FeatureSet-method |
| Probe information selector. | availProbeInfo getProbeInfo |
| Accessors for physical array coordinates. | getX getX,DBPDInfo-method getX,FeatureSet-method getX-methods getY getY,DBPDInfo-method getY,FeatureSet-method getY-methods |
| Density estimate | hist hist,ExpressionSet-method hist,FeatureSet-method hist-methods |
| Display a pseudo-image of a microarray chip | image image,FeatureSet-method image,PLMset-method image-methods |
| Summarization of SNP data | justSNPRMA |
| List XYS files | list.xysfiles |
| MA plots | MAplot MAplot,ExpressionSet-method MAplot,FeatureSet-method MAplot,matrix-method MAplot,PLMset-method MAplot,TilingFeatureSet-method MAplot-methods |
| Accessors and replacement methods for the intensity/PM/MM/BG matrices. | bg bg,FeatureSet-method bg,TilingFeatureSet-method bg<- bg<-,FeatureSet,ff_matrix-method bg<-,FeatureSet,matrix-method bg<-,TilingFeatureSet,array-method intensity intensity,FeatureSet-method intensity<- intensity<-,FeatureSet-method mm mm,FeatureSet-method mm,TilingFeatureSet-method mm<- mm<-,FeatureSet,ANY,ANY,ff_matrix-method mm<-,FeatureSet,ANY,ANY,matrix-method mm<-,TilingFeatureSet,ANY,ANY,array-method pm pm,FeatureSet-method pm,GenericFeatureSet-method pm,TilingFeatureSet-method pm<- pm<-,FeatureSet,ANY,ANY,ff_matrix-method pm<-,FeatureSet,ANY,ANY,matrix-method pm<-,GenericFeatureSet,ANY,ANY,ff_matrix-method pm<-,GenericFeatureSet,ANY,ANY,matrix-method pm<-,TilingFeatureSet,ANY,ANY,array-method |
| Accessors for PM, MM or background probes indices. | bgindex bgindex,DBPDInfo-method bgindex,FeatureSet-method mmindex mmindex,DBPDInfo-method mmindex,FeatureSet-method pmindex pmindex,DBPDInfo-method pmindex,FeatureSet-method pmindex,GenericFeatureSet-method pmindex,GenericPDInfo-method pmindex,stArrayDBPDInfo-method |
| Probe Sequeces | bgSequence bgSequence,DBPDInfo-method bgSequence,ExonFeatureSet-method bgSequence,FeatureSet-method bgSequence,GeneFeatureSet-method mmSequence mmSequence,AffySNPPDInfo-method mmSequence,DBPDInfo-method mmSequence,FeatureSet-method pmSequence pmSequence,AffyGenePDInfo-method pmSequence,AffySNPPDInfo-method pmSequence,DBPDInfo-method pmSequence,ExonFeatureSet-method pmSequence,FeatureSet-method pmSequence,GeneFeatureSet-method pmSequence,stArrayDBPDInfo-method |
| Defunct Functions in Package 'oligo' | coefs fitPLM oligo-defunct resids |
| Class '"oligoPLM"' | annotation,oligoPLM-method boxplot,oligoPLM-method coef,oligoPLM-method coefs.probe coefs.probe,oligoPLM-method geometry,oligoPLM-method image,oligoPLM-method manufacturer,oligoPLM-method method method,oligoPLM-method ncol,oligoPLM-method nprobes nprobes,oligoPLM-method nprobesets nprobesets,oligoPLM-method NUSE NUSE,oligoPLM-method oligoPLM oligoPLM-class opset2eset opset2eset,oligoPLM-method residuals,oligoPLM-method residualSE residualSE,oligoPLM-method RLE RLE,oligoPLM-method se se,oligoPLM-method se.probe se.probe,oligoPLM-method show,oligoPLM-method weights,oligoPLM-method |
| Methods for P/A Calls | paCalls paCalls,ExonFeatureSet-method paCalls,ExpressionFeatureSet-method paCalls,GeneFeatureSet-method |
| Methods for Log-Ratio plotting | plotM plotM,SnpQSet,character-method plotM,SnpQSet,integer-method plotM,SnpQSet,numeric-method plotM,TilingQSet,missing-method plotM-methods |
| Access the allele information for PM probes. | pmAllele pmAllele,AffySNPPDInfo-method pmAllele,SnpFeatureSet-method |
| Access the fragment length for PM probes. | pmFragmentLength pmFragmentLength,AffySNPPDInfo-method pmFragmentLength,SnpFeatureSet-method |
| Accessor to position information | pmOffset pmOffset,AffySNPPDInfo-method pmPosition pmPosition,ExpressionPDInfo-method pmPosition,FeatureSet-method pmPosition,TilingFeatureSet-method pmPosition,TilingPDInfo-method |
| Accessor to the strand information | pmStrand pmStrand,AffySNPPDInfo-method pmStrand,TilingFeatureSet-method |
| Accessor to feature names | probeNames probeNames,DBPDInfo-method probeNames,ExonFeatureSet-method probeNames,FeatureSet-method probeNames,GeneFeatureSet-method probeNames,stArrayDBPDInfo-method probesetNames probesetNames,FeatureSet-method |
| Parser to CEL files | cleanPlatformName read.celfiles read.celfiles2 |
| Parser to XYS files | read.xysfiles read.xysfiles2 |
| Read summaries generated by crlmm | readSummaries |
| RMA - Robust Multichip Average algorithm | rma rma,ExonFeatureSet-method rma,ExpressionFeatureSet-method rma,GeneFeatureSet-method rma,GenericFeatureSet-method rma,HTAFeatureSet-method rma,SnpCnvFeatureSet-method rma-methods |
| Date of scan | runDate runDate,FeatureSet-method runDate-methods |
| Create design matrix for sequences | sequenceDesignMatrix |
| Preprocessing SNP Arrays | snprma |
| Tools for microarray preprocessing. | backgroundCorrect backgroundCorrect,FeatureSet-method backgroundCorrect,ff_matrix-method backgroundCorrect,matrix-method backgroundCorrect-methods backgroundCorrectionMethods normalizationMethods normalize,FeatureSet-method normalize,ff_matrix-method normalize,matrix-method normalizeToTarget normalizeToTarget,ff_matrix-method normalizeToTarget,matrix-method normalizeToTarget-methods summarizationMethods summarize summarize,ff_matrix-method summarize,matrix-method summarize-methods |
