Oligonucleotide Arrays


[Package List] [Top]

Documentation for package ‘oligo’ version 1.6.0

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

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