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:Benilton Carvalho and Rafael Irizarry

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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

Uses libs:

zlib– Compression library

On BioConductor:oligo-1.71.0(bioc 3.21)oligo-1.70.0(bioc 3.20)

microarray onechannel twochannel preprocessing snp differentialexpression exonarray geneexpression dataimport zlib

10.32 score 3 stars 11 packages 532 scripts 2.6k downloads 204 mentions 88 exports 55 dependencies

Last updated 2 months agofrom:b720ab9af6. Checks:OK: 1 ERROR: 1 WARNING: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 17 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	Nov 29 2024
R-4.4-mac-x86_64	WARNING	Dec 17 2024
R-4.4-mac-aarch64	WARNING	Dec 17 2024
R-4.3-win-x86_64	WARNING	Nov 29 2024
R-4.3-mac-x86_64	WARNING	Dec 17 2024
R-4.3-mac-aarch64	WARNING	Dec 17 2024

Exports:annotation availProbeInfo backgroundCorrect backgroundCorrectionMethods basecontent basicPLM basicRMA bg bg<-bgSequence boxplot cleanPlatformName coef coefs.probe crlmm darkColors db divColors exprs exprs<-fitProbeLevelModel geometry getAffinitySplineCoefficients getBaseProfile getContainer getCrlmmSummaries getNetAffx getNgsColorsInfo getPD getPlatformDesign getProbeInfo getX getY hist image intensity justCRLMM justSNPRMA list.xysfiles manufacturer MAplot method mm mm<-mmindex mmSequence ncol normalizationMethods normalize normalizeToTarget nprobes nprobesets NUSE opset2eset paCalls plotM pm pm<-pmAllele pmChr pmFragmentLength pmindex pmOffset pmPosition pmSequence pmStrand probeNames probesetNames read.celfiles read.celfiles2 read.xysfiles read.xysfiles2 readSummaries residuals residualSE RLE rma runDate se se.probe seqColors seqColors2 sequenceDesignMatrix show snprma summarizationMethods summarize weights

Dependencies:abind affxparser affyio askpass Biobase BiocGenerics BiocManager Biostrings bit bit64 blob cachem cli codetools cpp11 crayon curl DBI DelayedArray fastmap ff foreach generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr IRanges iterators jsonlite lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime oligoClasses openssl pkgconfig plogr preprocessCore R6 rlang RSQLite S4Arrays S4Vectors SparseArray SummarizedExperiment sys UCSC.utils vctrs XVector zlibbioc

oligo User's Guide

Rendered fromoug.Rnwusingutils::Sweaveon Dec 17 2024.

Last update: 2020-01-07
Started: 2015-04-07

Citation

Development and contributors

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