# Preprocessing tools for oligonucleotide arrays.

## Documentation for package ‘oligo’ version 1.12.2

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

B C D G H I J L M N P R S

## -- --

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

## -- B --

backgroundCorrect | Tools for microarray preprocessing
backgroundCorrect-method | Tools for microarray preprocessing
backgroundCorrect-methods | Tools for microarray preprocessing
basecontent | Sequence Base Contents
basicRMA | Simplified Interface to RMA
bg | Accessors and replacement methods for the PM/MM/BG matrices.
bg-method | Accessors and replacement methods for the PM/MM/BG matrices.
bg<- | Accessors and replacement methods for the PM/MM/BG matrices.
bg<--method | Accessors and replacement methods for the 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-method | Boxplot
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
crlmm | Genotype Calls

## -- D --

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

## -- G --

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
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
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-method | Density estimate
hist-methods | Density estimate

## -- I --

image-method | Display a pseudo-image of a microarray chip
image-methods | Display a pseudo-image of a microarray chip

## -- J --

justCRLMM | Genotype Calls
justSNPRMA | Summarization of SNP data

## -- L --

list.xysfiles | List XYS files

## -- M --

MAplot | MA plots
MAplot-method | MA plots
MAplot-methods | MA plots
mm | Accessors and replacement methods for the PM/MM/BG matrices.
mm-method | Accessors and replacement methods for the PM/MM/BG matrices.
mm<- | Accessors and replacement methods for the PM/MM/BG matrices.
mm<--method | Accessors and replacement methods for the 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 --

normalize | Tools for microarray preprocessing
normalize-method | Tools for microarray preprocessing
normalize-methods | Tools for microarray preprocessing
normalizeToTarget | Tools for microarray preprocessing
normalizeToTarget-method | Tools for microarray preprocessing
normalizeToTarget-methods | Tools for microarray preprocessing

## -- P --

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 PM/MM/BG matrices.
pm-method | Accessors and replacement methods for the PM/MM/BG matrices.
pm<- | Accessors and replacement methods for the PM/MM/BG matrices.
pm<--method | Accessors and replacement methods for the 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

## -- 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
rma | RMA - Robust Multichip Average algorithm
rma-method | RMA - Robust Multichip Average algorithm
rma-methods | RMA - Robust Multichip Average algorithm

## -- S --

seqColors | Create set of colors, interpolating through a set of preferred colors.
sequenceDesignMatrix | Create design matrix for sequences
snprma | Preprocessing SNP Arrays
summarize | Tools for microarray preprocessing
summarize-method | Tools for microarray preprocessing
summarize-methods | Tools for microarray preprocessing