Entry: DBPDInfo-class
Aliases: initialize,DBPDInfo-method DBPDInfo-class AffySNPPDInfo-class AffySNPCNVPDInfo-class show,DBPDInfo-method AffyExpressionPDInfo-class AffyTilingPDInfo-class AffyGenePDInfo-class AffyExonPDInfo-class AffySTPDInfo-class SNPPDInfo-class SNPCNVPDInfo-class NgsTilingPDInfo-class TilingPDInfo-class ExpressionPDInfo-class NgsExpressionPDInfo-class
Keywords: classes
Description: Class "DBPDInfo"
URL: ../../../library/oligoClasses/html/DBPDInfo-class.html

Entry: FeatureSet-class
Aliases: show,FeatureSet-method FeatureSet-class initialize,FeatureSet-method GeneFeatureSet-class ExpressionFeatureSet-class ExonFeatureSet-class SnpFeatureSet-class SnpCnvFeatureSet-class TilingFeatureSet-class
Keywords: classes
Description: "FeatureSet" and "FeatureSet" Extensions
URL: ../../../library/oligoClasses/html/FeatureSetExtensions-class.html

Entry: mmindex
Aliases: mmindex mmindex,FeatureSet-method mmindex,DBPDInfo-method pmindex pmindex,FeatureSet-method pmindex,DBPDInfo-method bgindex bgindex,FeatureSet-method bgindex,DBPDInfo-method
Keywords: manip
Description: Accessors for PM, MM or background probes indices.
URL: ../../../library/oligoClasses/html/Index-methods.html

Entry: geometry
Aliases: geometry geometry,DBPDInfo-method
Keywords: manip
Description: Array Geometry Information
URL: ../../../library/oligoClasses/html/PDInfo-methods.html

Entry: QuantificationSet-class
Aliases: QuantificationSet-class
Keywords: classes
Description: Class "QuantificationSet"
URL: ../../../library/oligoClasses/html/QuantificationSet-class.html

Entry: mmSequence
Aliases: mmSequence mmSequence,DBPDInfo-method mmSequence,FeatureSet-method pmSequence pmSequence,DBPDInfo-method pmSequence,FeatureSet-method pmSequence,AffySNPPDInfo-method bgSequence bgSequence,FeatureSet-method bgSequence,DBPDInfo-method
Keywords: manip
Description: Probe Sequeces
URL: ../../../library/oligoClasses/html/Sequences-methods.html

Entry: calls
Aliases: calls calls,SnpCallSet-method calls<- calls<-,SnpCallSet,matrix-method callsConfidence callsConfidence,SnpCallSet-method callsConfidence<- callsConfidence<-,SnpCallSet,matrix-method
Keywords: manip
Description: Accessors for SnpCallSet
URL: ../../../library/oligoClasses/html/SnpCallSet-methods.html

Entry: SnpCallSetPlus-class
Aliases: SnpCallSetPlus-class SnpCnvCallSetPlus-class initialize,SnpCallSetPlus-method initialize,SnpCnvCallSetPlus-method coerce,SnpCallSetPlus,oligoSnpSet-method db,SnpCallSetPlus-method
Keywords: classes
Description: Class "SnpCallSetPlus"
URL: ../../../library/oligoClasses/html/SnpCallSetPlus-class.html

Entry: SnpCnvQSet-class
Aliases: SnpCnvQSet-class
Keywords: classes
Description: Class "SnpCnvQSet"
URL: ../../../library/oligoClasses/html/SnpCnvQSet-class.html

Entry: cnConfidence
Aliases: cnConfidence copyNumber cnConfidence<- copyNumber<- cnConfidence,SnpCopyNumberSet-method copyNumber,SnpCopyNumberSet-method cnConfidence<-,SnpCopyNumberSet,matrix-method copyNumber<-,SnpCopyNumberSet,matrix-method
Keywords: manip
Description: Accessors for SnpCopyNumberSet objects
URL: ../../../library/oligoClasses/html/SnpCopyNumberSet-methods.html

Entry: SnpLevelSet-class
Aliases: SnpLevelSet-class calls,SnpLevelSet-method calls<-,SnpLevelSet,matrix-method callsConfidence,SnpLevelSet-method callsConfidence<-,SnpLevelSet,matrix-method chromosome,SnpLevelSet-method chromosome<-,SnpLevelSet,character-method cnConfidence,SnpLevelSet-method cnConfidence<-,SnpLevelSet,matrix-method combine,SnpLevelSet,SnpLevelSet-method copyNumber,SnpLevelSet-method copyNumber<-,SnpLevelSet,matrix-method db,SnpLevelSet-method position,SnpLevelSet-method
Keywords: classes
Description: Class "SnpLevelSet"
URL: ../../../library/oligoClasses/html/SnpLevelSet-class.html

Entry: SnpQSet-class
Aliases: SnpQSet-class initialize,SnpQSet-method
Keywords: classes
Description: Class "SnpQSet"
URL: ../../../library/oligoClasses/html/SnpQSet-class.html

Entry: getA
Aliases: getA getM getA,SnpQSet-method getM,SnpQSet-method getA,SnpCnvQSet-method getM,SnpCnvQSet-method getM,TilingFeatureSet2-method getA,TilingFeatureSet2-method
Keywords: manip
Description: Compute average log-intensities / log-ratios
URL: ../../../library/oligoClasses/html/SnpQSet-methods.html

Entry: SnpCallSet-class
Aliases: SnpCallSet-class initialize,SnpCallSet-method SnpCallSet-methods SnpCopyNumberSet-class SnpCopyNumberSet-methods initialize,SnpCopyNumberSet-method
Keywords: classes methods
Description: "SnpSet" Extensions
URL: ../../../library/oligoClasses/html/SnpSetExtensions-class.html

Entry: affyPlatforms
Aliases: affyPlatforms
Keywords: list misc
Description: Available Affymetrix platforms for SNP arrays
URL: ../../../library/oligoClasses/html/affyPlatforms.html

Entry: chromosome
Aliases: chromosome chromosome<- chromosome<-,AnnotatedDataFrame,character-method pmChr pmChr,FeatureSet-method
Keywords: manip
Description: Accessor for chromosome information
URL: ../../../library/oligoClasses/html/chromosome.html

Entry: efsExample
Aliases: efsExample
Keywords: datasets
Description: ExpressionFeatureSet Object
URL: ../../../library/oligoClasses/html/data-efsExample.html

Entry: scqsExample
Aliases: scqsExample
Keywords: datasets
Description: SnpCnvQSet Example
URL: ../../../library/oligoClasses/html/data-scqsExample.html

Entry: sfsExample
Aliases: sfsExample
Keywords: datasets
Description: SnpFeatureSet Example
URL: ../../../library/oligoClasses/html/data-sfsExample.html

Entry: sqsExample
Aliases: sqsExample
Keywords: datasets
Description: SnpQSet Example
URL: ../../../library/oligoClasses/html/data-sqsExample.html

Entry: db
Aliases: db db-methods db,FeatureSet-method db,DBPDInfo-method db,SnpCallSet-method db,SnpCnvQSet-method db,SnpQSet-method
Keywords: methods
Description: Get the connection to the SQLite Database
URL: ../../../library/oligoClasses/html/db.html

Entry: exprs-methods
Aliases: exprs-methods exprs,FeatureSet-method se.exprs,FeatureSet-method
Keywords: methods
Description: Accessor for the 'exprs' slot
URL: ../../../library/oligoClasses/html/exprs-methods.html

Entry: genomeBuild
Aliases: genomeBuild genomeBuild,DBPDInfo-method genomeBuild,FeatureSet-method
Keywords: manip
Description: Genome Build Information
URL: ../../../library/oligoClasses/html/genomeBuild.html

Entry: getPlatformDesign
Aliases: getPlatformDesign getPD getPlatformDesign,FeatureSet-method
Keywords: manip
Description: Retrieve Platform Design object
URL: ../../../library/oligoClasses/html/getPlatformDesign.html

Entry: kind
Aliases: kind kind,AffySNPPDInfo-method kind,AffySNPCNVPDInfo-method kind,AffyExonPDInfo-method kind,ExpressionPDInfo-method kind,TilingPDInfo-method kind,AffyExpressionPDInfo-method kind,AffyGenePDInfo-method kind,FeatureSet-method
Keywords: manip
Description: Array type
URL: ../../../library/oligoClasses/html/kind.html

Entry: length-methods
Aliases: length-methods length,FeatureSet-method
Keywords: methods
Description: Number of samples for FeatureSet-like objects.
URL: ../../../library/oligoClasses/html/length-methods.html

Entry: manufacturer-methods
Aliases: manufacturer manufacturer-methods manufacturer,DBPDInfo-method manufacturer,FeatureSet-method
Keywords: methods
Description: Manufacturer ID for FeatureSet-like objects.
URL: ../../../library/oligoClasses/html/manufacturer-methods.html

Entry: oligoSnpSet-methods
Aliases: oligoSnpSet-class initialize,oligoSnpSet-method copyNumber,oligoSnpSet-method copyNumber<-,oligoSnpSet,matrix-method calls,oligoSnpSet-method calls<-,oligoSnpSet,matrix-method cnConfidence,oligoSnpSet-method cnConfidence<-,oligoSnpSet,matrix-method callsConfidence,oligoSnpSet-method callsConfidence<-,oligoSnpSet,matrix-method
Keywords: methods
Description: Methods for oligoSnpSet class
URL: ../../../library/oligoClasses/html/oligoSnpSet-methods.html

Entry: platform-methods
Aliases: platform platform-methods platform,FeatureSet-method
Keywords: methods
Description: Platform Information
URL: ../../../library/oligoClasses/html/platform-methods.html

Entry: pmAllele
Aliases: pmAllele pmAllele,SnpFeatureSet-method pmAllele,AffySNPPDInfo-method
Keywords: manip
Description: Access the allele information for PM probes.
URL: ../../../library/oligoClasses/html/pmAllele.html

Entry: pmFragmentLength-methods
Aliases: pmFragmentLength pmFragmentLength-methods pmFragmentLength,AffySNPPDInfo-method
Keywords: methods
Description: Information on Fragment Length
URL: ../../../library/oligoClasses/html/pmFragmentLength-methods.html

Entry: pmPosition
Aliases: pmPosition pmPosition,TilingFeatureSet-method pmPosition,ExpressionPDInfo-method pmPosition,TilingPDInfo-method pmOffset pmOffset,AffySNPPDInfo-method
Keywords: manip
Description: Accessor to position information
URL: ../../../library/oligoClasses/html/pmPosition.html

Entry: pmStrand
Aliases: pmStrand pmStrand,AffySNPPDInfo-method
Keywords: manip
Description: Accessor to the strand information
URL: ../../../library/oligoClasses/html/pmStrand.html

Entry: position
Aliases: position
Keywords: manip
Description: Accessor to position information
URL: ../../../library/oligoClasses/html/position.html

Entry: probeNames
Aliases: probeNames probeNames,FeatureSet-method probeNames,DBPDInfo-method
Keywords: manip
Description: Accessor to feature names
URL: ../../../library/oligoClasses/html/probeNames.html

Entry: sampleNames-methods
Aliases: sampleNames-methods sampleNames,FeatureSet-method
Keywords: methods
Description: Sample names for FeatureSet-like objects
URL: ../../../library/oligoClasses/html/sampleNames-methods.html

Entry: antisenseThetaA
Aliases: antisenseThetaA antisenseThetaB senseThetaA senseThetaB antisenseThetaA,SnpQSet-method antisenseThetaB,SnpQSet-method senseThetaA,SnpQSet-method senseThetaB,SnpQSet-method thetaA thetaB thetaA,SnpCnvQSet-method thetaB,SnpCnvQSet-method
Keywords: manip
Description: Summarized Measures for SNP
URL: ../../../library/oligoClasses/html/snprmaSummaries.html
