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

Files in this package

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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