# Preprocessing tools for oligonucleotide arrays

## Documentation for package ‘oligo’ version 1.60.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D F G H I J L M N O P R S W

oligo-package | The oligo package: a tool for low-level analysis of oligonucleotide arrays

## -- A --

annotation-method | Class '"oligoPLM"'
availProbeInfo | Probe information selector.

## -- B --

backgroundCorrect | Tools for microarray preprocessing.
backgroundCorrect-method | Tools for microarray preprocessing.
backgroundCorrect-methods | Tools for microarray preprocessing.
backgroundCorrectionMethods | Tools for microarray preprocessing.
basecontent | Sequence Base Contents
basicPLM | Simplified interface to PLM.
basicRMA | Simplified interface to RMA.
bg | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
bg-method | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
bg<- | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
bg<--method | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
bgindex | Accessors for PM, MM or background probes indices.
bgindex-method | Accessors for PM, MM or background probes indices.
bgSequence | Probe Sequeces
bgSequence-method | Probe Sequeces
boxplot | Boxplot
boxplot-method | Boxplot
boxplot-method | Class '"oligoPLM"'
boxplot-methods | Boxplot

## -- C --

chromosome | Accessor for chromosome information
chromosome<- | Accessor for chromosome information
chromosome<--method | Accessor for chromosome information
cleanPlatformName | Parser to CEL files
coef-method | Class '"oligoPLM"'
coefs | Defunct Functions in Package 'oligo'
coefs.probe | Class '"oligoPLM"'
coefs.probe-method | Class '"oligoPLM"'
crlmm | Genotype Calls

## -- D --

darkColors | Create set of colors, interpolating through a set of preferred colors.
divColors | Create set of colors, interpolating through a set of preferred colors.

## -- F --

fitPLM | Defunct Functions in Package 'oligo'
fitProbeLevelModel | Tool to fit Probe Level Models.

## -- G --

geometry-method | Class '"oligoPLM"'
getAffinitySplineCoefficients | Estimate affinity coefficients.
getBaseProfile | Compute and plot nucleotide profile.
getContainer | Get container information for NimbleGen Tiling Arrays.
getContainer-method | Get container information for NimbleGen Tiling Arrays.
getContainer-methods | Get container information for NimbleGen Tiling Arrays.
getCrlmmSummaries | Function to get CRLMM summaries saved to disk
getNetAffx | NetAffx Biological Annotations
getNetAffx-method | NetAffx Biological Annotations
getNetAffx-methods | NetAffx Biological Annotations
getNgsColorsInfo | Helper function to extract color information for filenames on NimbleGen arrays.
getPD | Retrieve Platform Design object
getPlatformDesign | Retrieve Platform Design object
getPlatformDesign-method | Retrieve Platform Design object
getProbeInfo | Probe information selector.
getX | Accessors for physical array coordinates.
getX-method | Accessors for physical array coordinates.
getX-methods | Accessors for physical array coordinates.
getY | Accessors for physical array coordinates.
getY-method | Accessors for physical array coordinates.
getY-methods | Accessors for physical array coordinates.

## -- H --

hist | Density estimate
hist-method | Density estimate
hist-methods | Density estimate

## -- I --

image | Display a pseudo-image of a microarray chip
image-method | Display a pseudo-image of a microarray chip
image-method | Class '"oligoPLM"'
image-methods | Display a pseudo-image of a microarray chip
intensity | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
intensity-method | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
intensity<- | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
intensity<--method | Accessors and replacement methods for the intensity/PM/MM/BG matrices.

## -- J --

justCRLMM | Genotype Calls
justSNPRMA | Summarization of SNP data

## -- L --

list.xysfiles | List XYS files

## -- M --

manufacturer-method | Class '"oligoPLM"'
MAplot | MA plots
MAplot-method | MA plots
MAplot-methods | MA plots
method | Class '"oligoPLM"'
method-method | Class '"oligoPLM"'
mm | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
mm-method | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
mm<- | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
mm<--method | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
mmindex | Accessors for PM, MM or background probes indices.
mmindex-method | Accessors for PM, MM or background probes indices.
mmSequence | Probe Sequeces
mmSequence-method | Probe Sequeces

## -- N --

ncol-method | Class '"oligoPLM"'
normalizationMethods | Tools for microarray preprocessing.
normalize-method | Tools for microarray preprocessing.
normalizeToTarget | Tools for microarray preprocessing.
normalizeToTarget-method | Tools for microarray preprocessing.
normalizeToTarget-methods | Tools for microarray preprocessing.
nprobes | Class '"oligoPLM"'
nprobes-method | Class '"oligoPLM"'
nprobesets | Class '"oligoPLM"'
nprobesets-method | Class '"oligoPLM"'
NUSE | Class '"oligoPLM"'
NUSE-method | Class '"oligoPLM"'

## -- O --

oligo-defunct | Defunct Functions in Package 'oligo'
oligoPLM | Class '"oligoPLM"'
oligoPLM-class | Class '"oligoPLM"'
opset2eset | Class '"oligoPLM"'
opset2eset-method | Class '"oligoPLM"'

## -- P --

paCalls | Methods for P/A Calls
paCalls-method | Methods for P/A Calls
plotM | Methods for Log-Ratio plotting
plotM-method | Methods for Log-Ratio plotting
plotM-methods | Methods for Log-Ratio plotting
pm | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
pm-method | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
pm<- | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
pm<--method | Accessors and replacement methods for the intensity/PM/MM/BG matrices.
pmAllele | Access the allele information for PM probes.
pmAllele-method | Access the allele information for PM probes.
pmChr | Accessor for chromosome information
pmChr-method | Accessor for chromosome information
pmFragmentLength | Access the fragment length for PM probes.
pmFragmentLength-method | Access the fragment length for PM probes.
pmindex | Accessors for PM, MM or background probes indices.
pmindex-method | Accessors for PM, MM or background probes indices.
pmOffset | Accessor to position information
pmOffset-method | Accessor to position information
pmPosition | Accessor to position information
pmPosition-method | Accessor to position information
pmSequence | Probe Sequeces
pmSequence-method | Probe Sequeces
pmStrand | Accessor to the strand information
pmStrand-method | Accessor to the strand information
probeNames | Accessor to feature names
probeNames-method | Accessor to feature names
probesetNames | Accessor to feature names
probesetNames-method | Accessor to feature names

## -- R --

read.celfiles | Parser to CEL files
read.celfiles2 | Parser to CEL files
read.xysfiles | Parser to XYS files
read.xysfiles2 | Parser to XYS files
readSummaries | Read summaries generated by crlmm
resids | Defunct Functions in Package 'oligo'
residuals-method | Class '"oligoPLM"'
residualSE | Class '"oligoPLM"'
residualSE-method | Class '"oligoPLM"'
RLE | Class '"oligoPLM"'
RLE-method | Class '"oligoPLM"'
rma | RMA - Robust Multichip Average algorithm
rma-method | RMA - Robust Multichip Average algorithm
rma-methods | RMA - Robust Multichip Average algorithm
runDate | Date of scan
runDate-method | Date of scan
runDate-methods | Date of scan

## -- S --

se | Class '"oligoPLM"'
se-method | Class '"oligoPLM"'
se.probe | Class '"oligoPLM"'
se.probe-method | Class '"oligoPLM"'
seqColors | Create set of colors, interpolating through a set of preferred colors.
seqColors2 | Create set of colors, interpolating through a set of preferred colors.
sequenceDesignMatrix | Create design matrix for sequences
show-method | Class '"oligoPLM"'
snprma | Preprocessing SNP Arrays
summarizationMethods | Tools for microarray preprocessing.
summarize | Tools for microarray preprocessing.
summarize-method | Tools for microarray preprocessing.
summarize-methods | Tools for microarray preprocessing.

## -- W --

weights-method | Class '"oligoPLM"'