Preprocessing tools for oligonucleotide arrays.

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Documentation for package ‘oligo’ version 1.28.3

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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 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.
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"'

-- 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"'