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).

Author
Benilton Carvalho and Rafael Irizarry
Date of publication
None
Maintainer
Benilton Carvalho <benilton@unicamp.br>
License
LGPL (>= 2)
Version
1.38.0

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