Classes for high-throughput SNP arrays


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Documentation for package ‘oligoClasses’ version 1.6.0

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A B C D E F G I K L M N O P Q S T

-- A --

AffyExonPDInfo-class Class "DBPDInfo"
AffyExpressionPDInfo-class Class "DBPDInfo"
AffyGenePDInfo-class Class "DBPDInfo"
affyPlatforms Available Affymetrix platforms for SNP arrays
AffySNPCNVPDInfo-class Class "DBPDInfo"
AffySNPPDInfo-class Class "DBPDInfo"
AffySTPDInfo-class Class "DBPDInfo"
AffyTilingPDInfo-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 --

bgindex Accessors for PM, MM or background probes indices.
bgindex,DBPDInfo-method Accessors for PM, MM or background probes indices.
bgindex,FeatureSet-method Accessors for PM, MM or background probes indices.
bgSequence Probe Sequeces
bgSequence,DBPDInfo-method Probe Sequeces
bgSequence,FeatureSet-method Probe Sequeces

-- C --

calls Accessors for SnpCallSet
calls,oligoSnpSet-method Methods for oligoSnpSet class
calls,SnpCallSet-method Accessors for SnpCallSet
calls,SnpLevelSet-method Class "SnpLevelSet"
calls<- Accessors for SnpCallSet
calls<-,oligoSnpSet,matrix-method Methods for oligoSnpSet class
calls<-,SnpCallSet,matrix-method Accessors for SnpCallSet
calls<-,SnpLevelSet,matrix-method Class "SnpLevelSet"
callsConfidence Accessors for SnpCallSet
callsConfidence,oligoSnpSet-method Methods for oligoSnpSet class
callsConfidence,SnpCallSet-method Accessors for SnpCallSet
callsConfidence,SnpLevelSet-method Class "SnpLevelSet"
callsConfidence<- Accessors for SnpCallSet
callsConfidence<-,oligoSnpSet,matrix-method Methods for oligoSnpSet class
callsConfidence<-,SnpCallSet,matrix-method Accessors for SnpCallSet
callsConfidence<-,SnpLevelSet,matrix-method Class "SnpLevelSet"
chromosome Accessor for chromosome information
chromosome,SnpLevelSet-method Class "SnpLevelSet"
chromosome<- Accessor for chromosome information
chromosome<-,AnnotatedDataFrame,character-method Accessor for chromosome information
chromosome<-,SnpLevelSet,character-method Class "SnpLevelSet"
cnConfidence Accessors for SnpCopyNumberSet objects
cnConfidence,oligoSnpSet-method Methods for oligoSnpSet class
cnConfidence,SnpCopyNumberSet-method Accessors for SnpCopyNumberSet objects
cnConfidence,SnpLevelSet-method Class "SnpLevelSet"
cnConfidence<- Accessors for SnpCopyNumberSet objects
cnConfidence<-,oligoSnpSet,matrix-method Methods for oligoSnpSet class
cnConfidence<-,SnpCopyNumberSet,matrix-method Accessors for SnpCopyNumberSet objects
cnConfidence<-,SnpLevelSet,matrix-method Class "SnpLevelSet"
coerce,SnpCallSetPlus,oligoSnpSet-method Class "SnpCallSetPlus"
combine,SnpLevelSet,SnpLevelSet-method Class "SnpLevelSet"
copyNumber Accessors for SnpCopyNumberSet objects
copyNumber,oligoSnpSet-method Methods for oligoSnpSet class
copyNumber,SnpCopyNumberSet-method Accessors for SnpCopyNumberSet objects
copyNumber,SnpLevelSet-method Class "SnpLevelSet"
copyNumber<- Accessors for SnpCopyNumberSet objects
copyNumber<-,oligoSnpSet,matrix-method Methods for oligoSnpSet class
copyNumber<-,SnpCopyNumberSet,matrix-method Accessors for SnpCopyNumberSet objects
copyNumber<-,SnpLevelSet,matrix-method Class "SnpLevelSet"

-- D --

db Get the connection to the SQLite Database
db,DBPDInfo-method Get the connection to the SQLite Database
db,FeatureSet-method Get the connection to the SQLite Database
db,SnpCallSet-method Get the connection to the SQLite Database
db,SnpCallSetPlus-method Class "SnpCallSetPlus"
db,SnpCnvQSet-method Get the connection to the SQLite Database
db,SnpLevelSet-method Class "SnpLevelSet"
db,SnpQSet-method Get the connection to the SQLite Database
db-methods Get the connection to the SQLite Database
DBPDInfo-class Class "DBPDInfo"

-- E --

efsExample ExpressionFeatureSet Object
ExonFeatureSet-class "FeatureSet" and "FeatureSet" Extensions
ExpressionFeatureSet-class "FeatureSet" and "FeatureSet" Extensions
ExpressionPDInfo-class Class "DBPDInfo"
exprs,FeatureSet-method Accessor for the 'exprs' slot
exprs-methods Accessor for the 'exprs' slot

-- F --

FeatureSet-class "FeatureSet" and "FeatureSet" Extensions

-- G --

GeneFeatureSet-class "FeatureSet" and "FeatureSet" Extensions
genomeBuild Genome Build Information
genomeBuild,DBPDInfo-method Genome Build Information
genomeBuild,FeatureSet-method Genome Build Information
geometry Array Geometry Information
geometry,DBPDInfo-method Array Geometry Information
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
getA,TilingFeatureSet2-method Compute average log-intensities / log-ratios
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,TilingFeatureSet2-method Compute average log-intensities / log-ratios
getPD Retrieve Platform Design object
getPlatformDesign Retrieve Platform Design object
getPlatformDesign,FeatureSet-method Retrieve Platform Design object

-- I --

initialize,DBPDInfo-method Class "DBPDInfo"
initialize,FeatureSet-method "FeatureSet" and "FeatureSet" Extensions
initialize,oligoSnpSet-method Methods for oligoSnpSet class
initialize,SnpCallSet-method "SnpSet" Extensions
initialize,SnpCallSetPlus-method Class "SnpCallSetPlus"
initialize,SnpCnvCallSetPlus-method Class "SnpCallSetPlus"
initialize,SnpCopyNumberSet-method "SnpSet" Extensions
initialize,SnpQSet-method Class "SnpQSet"

-- K --

kind Array type
kind,AffyExonPDInfo-method 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,FeatureSet-method Array type
kind,TilingPDInfo-method Array type

-- L --

length,FeatureSet-method Number of samples for FeatureSet-like objects.
length-methods Number of samples for FeatureSet-like objects.

-- M --

manufacturer Manufacturer ID for FeatureSet-like objects.
manufacturer,DBPDInfo-method Manufacturer ID for FeatureSet-like objects.
manufacturer,FeatureSet-method Manufacturer ID for FeatureSet-like objects.
manufacturer-methods Manufacturer ID for FeatureSet-like objects.
mmindex Accessors for PM, MM or background probes indices.
mmindex,DBPDInfo-method Accessors for PM, MM or background probes indices.
mmindex,FeatureSet-method Accessors for PM, MM or background probes indices.
mmSequence Probe Sequeces
mmSequence,DBPDInfo-method Probe Sequeces
mmSequence,FeatureSet-method Probe Sequeces

-- N --

NgsExpressionPDInfo-class Class "DBPDInfo"
NgsTilingPDInfo-class Class "DBPDInfo"

-- O --

oligoSnpSet-class Methods for oligoSnpSet class

-- P --

platform Platform Information
platform,FeatureSet-method Platform Information
platform-methods Platform Information
pmAllele Access the allele information for PM probes.
pmAllele,AffySNPPDInfo-method Access the allele information for PM probes.
pmAllele,SnpFeatureSet-method Access the allele information for PM probes.
pmChr Accessor for chromosome information
pmChr,FeatureSet-method Accessor for chromosome information
pmFragmentLength Information on Fragment Length
pmFragmentLength,AffySNPPDInfo-method Information on Fragment Length
pmFragmentLength-methods Information on Fragment Length
pmindex Accessors for PM, MM or background probes indices.
pmindex,DBPDInfo-method Accessors for PM, MM or background probes indices.
pmindex,FeatureSet-method Accessors for PM, MM or background probes indices.
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,AffySNPPDInfo-method Probe Sequeces
pmSequence,DBPDInfo-method Probe Sequeces
pmSequence,FeatureSet-method Probe Sequeces
pmStrand Accessor to the strand information
pmStrand,AffySNPPDInfo-method Accessor to the strand information
position Accessor to position information
position,SnpLevelSet-method Class "SnpLevelSet"
probeNames Accessor to feature names
probeNames,DBPDInfo-method Accessor to feature names
probeNames,FeatureSet-method Accessor to feature names

-- Q --

QuantificationSet-class Class "QuantificationSet"

-- S --

sampleNames,FeatureSet-method Sample names for FeatureSet-like objects
sampleNames-methods Sample names for FeatureSet-like objects
scqsExample SnpCnvQSet Example
se.exprs,FeatureSet-method Accessor for the 'exprs' slot
senseThetaA Summarized Measures for SNP
senseThetaA,SnpQSet-method Summarized Measures for SNP
senseThetaB Summarized Measures for SNP
senseThetaB,SnpQSet-method Summarized Measures for SNP
sfsExample SnpFeatureSet Example
show,DBPDInfo-method Class "DBPDInfo"
show,FeatureSet-method "FeatureSet" and "FeatureSet" Extensions
SnpCallSet-class "SnpSet" Extensions
SnpCallSet-methods "SnpSet" Extensions
SnpCallSetPlus-class Class "SnpCallSetPlus"
SnpCnvCallSetPlus-class Class "SnpCallSetPlus"
SnpCnvFeatureSet-class "FeatureSet" and "FeatureSet" Extensions
SNPCNVPDInfo-class Class "DBPDInfo"
SnpCnvQSet-class Class "SnpCnvQSet"
SnpCopyNumberSet-class "SnpSet" Extensions
SnpCopyNumberSet-methods "SnpSet" Extensions
SnpFeatureSet-class "FeatureSet" and "FeatureSet" Extensions
SnpLevelSet-class Class "SnpLevelSet"
SNPPDInfo-class Class "DBPDInfo"
SnpQSet-class Class "SnpQSet"
sqsExample SnpQSet Example

-- T --

thetaA Summarized Measures for SNP
thetaA,SnpCnvQSet-method Summarized Measures for SNP
thetaB Summarized Measures for SNP
thetaB,SnpCnvQSet-method Summarized Measures for SNP
TilingFeatureSet-class "FeatureSet" and "FeatureSet" Extensions
TilingPDInfo-class Class "DBPDInfo"