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

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

Entry: FeatureSet-class
Aliases: FeatureSet-class
Keywords: classes
Description: Classes for Feature level data
URL: ../../../library/oligoClasses/html/FeatureSet-class.html

Entry: ExonFeatureSet-class
Aliases: ExpressionFeatureSet-class ExonFeatureSet-class SnpFeatureSet-class TilingFeatureSet-class
Keywords: classes
Description: "FeatureSet" Extensions
URL: ../../../library/oligoClasses/html/FeatureSetExtensions-class.html

Entry: GeneFeatureSet-class
Aliases: GeneFeatureSet-class
Keywords: classes
Description: Class GeneFeatureSet
URL: ../../../library/oligoClasses/html/GeneSTFeatureSet-class.html

Entry: PDInfo-class
Aliases: PDInfo-class AffyExpressionPDInfo-class AffyTilingPDInfo-class SNPPDInfo-class SNPCNVPDInfo-class NgsTilingPDInfo-class TilingPDInfo-class ExpressionPDInfo-class NgsExpressionPDInfo-class
Keywords: classes
Description: Classes "PDInfo" and "SNPPDInfo"
URL: ../../../library/oligoClasses/html/PDInfo-class.html

Entry: QuantificationSet-class
Aliases: QuantificationSet-class
Keywords: classes
Description: Class "QuantificationSet"
URL: ../../../library/oligoClasses/html/QuantificationSet-class.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 calculateCopyNumber,SnpCallSetPlus-method 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: SnpCnvFeatureSet-class
Aliases: SnpCnvFeatureSet-class
Keywords: classes
Description: Class "SnpCnvFeatureSet"
URL: ../../../library/oligoClasses/html/SnpCnvFeatureSet-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: 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: TilingQSet-class
Aliases: TilingQSet-class initialize,TilingQSet-method
Keywords: classes
Description: Class "TilingQSet"
URL: ../../../library/oligoClasses/html/TilingQSet-class.html

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

Entry: calculateCopyNumber
Aliases: calculateCopyNumber
Keywords: methods
Description: Calculates copy number as the average of SNP-level summaries from the A and B alleles
URL: ../../../library/oligoClasses/html/calculateCopyNumber.html

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

Entry: db
Aliases: db db-methods db,SnpCallSet-method db,DBPDInfo-method
Keywords: methods
Description: Get the connection to the SQLite Database
URL: ../../../library/oligoClasses/html/db.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: platformDesign-class
Aliases: platformDesign-class
Keywords: classes
Description: Class "platformDesign"
URL: ../../../library/oligoClasses/html/platformDesign-class.html

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