Oligonucleotide Arrays

Documentation for package ‘oligo’ version 1.6.0

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A B C D E F G H I J K L M N O P R S T misc

-- --

oligo-package

The oligo package: a tool for analysis of oligonucleotide arrays

-- --

$,platformDesign-method

Internals

-- A --

AffySNPPDInfo-class	Class "DBPDInfo"
antisenseThetaA	Summarized Measures for SNP
antisenseThetaA,SnpQSet-method	Summarized Measures for SNP
antisenseThetaB	Summarized Measures for SNP
antisenseThetaB,SnpQSet-method	Summarized Measures for SNP

-- B --

basecontent	Sequence Base Contents
boxplot	Boxplot
boxplot,ExpressionSet-method	Boxplot
boxplot,FeatureSet-method	Boxplot

-- C --

cleanPlatformName	Parser to CEL files
crlmm	Genotype Calls

-- D --

db	Internals
db,DBPDInfo-method	Internals
db,FeatureSet-method	Internals
db,SnpCallSet-method	Internals
db,SnpCnvQSet-method	Internals
db,SnpCopyNumberSet-method	Internals
db,SnpFeatureSet-method	Internals
db,SnpQSet-method	Internals
DBPDInfo-class	Class "DBPDInfo"

-- E --

ExonFeatureSet-class	"FeatureSet" Extensions
ExpressionFeatureSet-class	"FeatureSet" Extensions
exprs,FeatureSet-method	Internals

-- F --

featureIndex	Indexes for features in the expression matrix
featureIndex,FeatureSet-method	Indexes for features in the expression matrix
featureInfo	Internals
featureInfo,platformDesign-method	Internals
featureNames,FeatureSet-method	Retrieve featureNames
featureNames-methods	Retrieve featureNames
FeatureSet-class	Classes for Feature level data

-- G --

geneNames,AffySNPPDInfo-method	Internals
geneNames,ExpressionPDInfo-method	Internals
geneNames,FeatureSet-method	Internals
geneNames,platformDesign-method	Internals
geneNames,TilingPDInfo-method	Internals
genomeBuild	Genome Build Information
genomeBuild,FeatureSet-method	Genome Build Information
genomeBuild,PDInfo-method	Genome Build Information
genomeBuild,TilingFeatureSet-method	Genome Build Information
geometry	List fields in the (pm/mm)feature table
geometry,PDInfo-method	List fields in the (pm/mm)feature table
getA	Compute average log-intensities / log-ratios
getA,SnpCnvQSet-method	Compute average log-intensities / log-ratios
getA,SnpQSet-method	Compute average log-intensities / log-ratios
getChrXIndex	Internals
getCrlmmSummaries	Function to get CRLMM summaries saved to disk
getGenotypeRegionParams	Internals
getM	Compute average log-intensities / log-ratios
getM,SnpCnvQSet-method	Compute average log-intensities / log-ratios
getM,SnpQSet-method	Compute average log-intensities / log-ratios
getM,TilingQSet-method	Compute average log-intensities / log-ratios
getPD	Retrieve Platform Design object
getPlatformDesign	Retrieve Platform Design object
getPlatformDesign,FeatureSet-method	Retrieve Platform Design object
getSnpFragmentLength	Internals

-- H --

hist	Density estimate
hist,ExpressionSet-method	Density estimate
hist,FeatureSet-method	Density estimate

-- I --

image	Display a Color Image
image,FeatureSet-method	Display a Color Image
initialize,DBPDInfo-method	Internals
initialize,FeatureSet-method	Internals
initialize,SnpCallSet-method	Internals
initialize,SnpCopyNumberSet-method	Internals
initialize,SnpQSet-method	Internals

-- J --

justCRLMM	Genotype Calls
justSNPRMA	Summarization of SNP data

-- K --

kind	Array type
kind,AffyExpressionPDInfo-method	Array type
kind,AffyGenePDInfo-method	Array type
kind,AffySNPCNVPDInfo-method	Array type
kind,AffySNPPDInfo-method	Array type
kind,ExpressionPDInfo-method	Array type
kind,platformDesign-method	Array type
kind,TilingPDInfo-method	Array type

-- L --

length,FeatureSet-method	Internals
list.celfiles	List CEL/XYS files
list.xysfiles	List CEL/XYS files
listFeatureFields	List fields in the (pm/mm)feature table
listFeatureFields,AffySNPPDInfo-method	List fields in the (pm/mm)feature table
listFeatureFields,PDInfo-method	List fields in the (pm/mm)feature table
listFeatureSetFields	List fields in the (pm/mm)feature table
listFeatureSetFields,AffySNPPDInfo-method	List fields in the (pm/mm)feature table
listFeatureSetFields,PDInfo-method	List fields in the (pm/mm)feature table

-- M --

manufacturer	Accessor to the manufacturer slot.
manufacturer,FeatureSet-method	Accessor to the manufacturer slot.
manufacturer,PDInfo-method	Accessor to the manufacturer slot.
manufacturer<-,FeatureSet-method	Accessor to the manufacturer slot.
MAplot	MA plots
MAplot,FeatureSet-method	MA plots
MAplot-methods	MA plots
mm	Accessor to the PM/MM matrices
mm,FeatureSet-method	Accessor to the PM/MM matrices
mm<-,FeatureSet,BufferedMatrix-method	Accessor to the PM/MM matrices
mm<-,FeatureSet,matrix-method	Accessor to the PM/MM matrices
mmindex	Extract PM or MM indexes
mmindex,AffySNPPDInfo-method	Extract PM or MM indexes
mmindex,ExpressionPDInfo-method	Extract PM or MM indexes
mmindex,FeatureSet-method	Extract PM or MM indexes
mmindex,platformDesign-method	Extract PM or MM indexes
mmindex,TilingPDInfo-method	Extract PM or MM indexes
mmSequence	Probe Sequeces
mmSequence,AffySNPPDInfo-method	Probe Sequeces
mmSequence,FeatureSet-method	Probe Sequeces
mmSequence,platformDesign-method	Probe Sequeces

-- N --

names,platformDesign-method	Internals
ncol	~~function to do ... ~~
ncol,platformDesign-method	~~function to do ... ~~
normalizeToSample	Internals
nProbes	Count number of probes
nProbes,AffySNPPDInfo-method	Count number of probes
nProbes,ExpressionPDInfo-method	Count number of probes
nProbes,platformDesign-method	Count number of probes
nProbes,TilingPDInfo-method	Count number of probes
nrow	~~function to do ... ~~
nrow,platformDesign-method	~~function to do ... ~~

-- O --

oligoSnpSet-class

"SnpSet" Extensions

-- P --

PDInfo-class	Classes "PDInfo" and "SNPPDInfo"
platform	Retrieve/replace platform information
platform,FeatureSet-method	Retrieve/replace platform information
platform<-,FeatureSet-method	Retrieve/replace platform information
platformDesign-class	Class "platformDesign"
platformDesignName	Internals
platformDesignName,FeatureSet-method	Internals
plotM	Methods for Log-Ratio plotting
plotM,SnpQSet,character-method	Methods for Log-Ratio plotting
plotM,SnpQSet,integer-method	Methods for Log-Ratio plotting
plotM,SnpQSet,numeric-method	Methods for Log-Ratio plotting
plotM,TilingQSet,missing-method	Methods for Log-Ratio plotting
plotM-methods	Methods for Log-Ratio plotting
pm	Accessor to the PM/MM matrices
pm,FeatureSet-method	Accessor to the PM/MM matrices
pm,SnpCnvFeatureSet-method	Accessor to the PM/MM matrices
pm<-,FeatureSet,BufferedMatrix-method	Accessor to the PM/MM matrices
pm<-,FeatureSet,matrix-method	Accessor to the PM/MM matrices
pmAllele	Access the allele information for PM probes.
pmAllele,AffySNPPDInfo-method	Access the allele information for PM probes.
pmAllele,PDInfo-method	Access the allele information for PM probes.
pmAllele,SnpFeatureSet-method	Access the allele information for PM probes.
pmChr	Accessor for chromosome information
pmChr,TilingFeatureSet-method	Accessor for chromosome information
pmindex	Extract PM or MM indexes
pmindex,AffySNPCNVPDInfo-method	Extract PM or MM indexes
pmindex,AffySNPPDInfo-method	Extract PM or MM indexes
pmindex,ExpressionPDInfo-method	Extract PM or MM indexes
pmindex,FeatureSet-method	Extract PM or MM indexes
pmindex,platformDesign-method	Extract PM or MM indexes
pmindex,SnpCnvFeatureSet-method	Extract PM or MM indexes
pmindex,TilingPDInfo-method	Extract PM or MM indexes
pmOffset	Accessor to position information
pmOffset,AffySNPPDInfo-method	Accessor to position information
pmPosition	Accessor to position information
pmPosition,ExpressionPDInfo-method	Accessor to position information
pmPosition,TilingFeatureSet-method	Accessor to position information
pmPosition,TilingPDInfo-method	Accessor to position information
pmSequence	Probe Sequeces
pmSequence,AffySNPCNVPDInfo-method	Probe Sequeces
pmSequence,AffySNPPDInfo-method	Probe Sequeces
pmSequence,ExpressionPDInfo-method	Probe Sequeces
pmSequence,FeatureSet-method	Probe Sequeces
pmSequence,platformDesign-method	Probe Sequeces
pmSequence,TilingPDInfo-method	Probe Sequeces
pmStrand	Accessor to the strand information
pmStrand,AffySNPPDInfo-method	Accessor to the strand information
position,SnpCallSet-method	Accessor to position information
position,TilingFeatureSet-method	Accessor to position information
probeNames	Accessor to feature names
probeNames,AffySNPPDInfo-method	Accessor to feature names
probeNames,ExpressionPDInfo-method	Accessor to feature names
probeNames,FeatureSet-method	Accessor to feature names
probeNames,platformDesign-method	Accessor to feature names
probeNames,TilingPDInfo-method	Accessor to feature names

-- R --

read.celfiles	Parser to CEL files
read.xysfiles	Parser to XYS files
readSummaries	Read summaries generated by crlmm
rma	RMA
rma,FeatureSet-method	RMA

-- S --

senseThetaA	Summarized Measures for SNP
senseThetaA,SnpQSet-method	Summarized Measures for SNP
senseThetaB	Summarized Measures for SNP
senseThetaB,SnpQSet-method	Summarized Measures for SNP
sequenceDesignMatrix	Create design matrix for sequences
show,FeatureSet-method	Internals
show,PDInfo-method	Internals
show,platformDesign-method	Internals
SnpCallSet-class	"SnpSet" Extensions
SnpCopyNumberSet-class	"SnpSet" Extensions
SnpFeatureSet-class	"FeatureSet" Extensions
SNPPDInfo-class	Classes "PDInfo" and "SNPPDInfo"
SnpQSet-class	Class "SnpQSet"
snprma	Preprocessing SNP Arrays

-- T --

TilingFeatureSet-class

"FeatureSet" Extensions

-- misc --

[,FeatureSet-method

Internals