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| AffyExpressionPDInfo-class | Classes "PDInfo" and "SNPPDInfo" |
| AffyGenePDInfo-class | Class AffyGenePDInfo |
| affyPlatforms | Available Affymetrix platforms for SNP arrays |
| AffySNPCNVPDInfo-class | Class "DBPDInfo" |
| AffySNPPDInfo-class | Class "DBPDInfo" |
| AffyTilingPDInfo-class | Classes "PDInfo" and "SNPPDInfo" |
| calculateCopyNumber | Calculates copy number as the average of SNP-level summaries from the A and B alleles |
| calculateCopyNumber,SnpCallSetPlus-method | Class "SnpCallSetPlus" |
| calls | Accessors for SnpCallSet |
| calls,oligoSnpSet-method | Methods for oligoSnpSet class |
| calls,SnpCallSet-method | Accessors for SnpCallSet |
| calls,SnpLevelSet-method | Class "SnpLevelSet" |
| 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<-,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<-,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<-,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<-,oligoSnpSet,matrix-method | Methods for oligoSnpSet class |
| copyNumber<-,SnpCopyNumberSet,matrix-method | Accessors for SnpCopyNumberSet objects |
| copyNumber<-,SnpLevelSet,matrix-method | Class "SnpLevelSet" |
| db | Get the connection to the SQLite Database |
| db,DBPDInfo-method | Get the connection to the SQLite Database |
| db,SnpCallSet-method | Get the connection to the SQLite Database |
| db,SnpCallSetPlus-method | Class "SnpCallSetPlus" |
| db,SnpLevelSet-method | Class "SnpLevelSet" |
| db-methods | Get the connection to the SQLite Database |
| DBPDInfo-class | Class "DBPDInfo" |
| ExonFeatureSet-class | "FeatureSet" Extensions |
| ExpressionFeatureSet-class | "FeatureSet" Extensions |
| ExpressionPDInfo-class | Classes "PDInfo" and "SNPPDInfo" |
| FeatureSet-class | Classes for Feature level data |
| GeneFeatureSet-class | Class GeneFeatureSet |
| 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 |
| NgsExpressionPDInfo-class | Classes "PDInfo" and "SNPPDInfo" |
| NgsTilingPDInfo-class | Classes "PDInfo" and "SNPPDInfo" |
| oligoSnpSet-class | Methods for oligoSnpSet class |
| PDInfo-class | Classes "PDInfo" and "SNPPDInfo" |
| platformDesign-class | Class "platformDesign" |
| position | Accessor to position information |
| position,SnpLevelSet-method | Class "SnpLevelSet" |
| QuantificationSet-class | Class "QuantificationSet" |
| SnpCallSet-class | "SnpSet" Extensions |
| SnpCallSet-methods | "SnpSet" Extensions |
| SnpCallSetPlus-class | Class "SnpCallSetPlus" |
| SnpCnvCallSetPlus-class | Class "SnpCallSetPlus" |
| SnpCnvFeatureSet-class | Class "SnpCnvFeatureSet" |
| SNPCNVPDInfo-class | Classes "PDInfo" and "SNPPDInfo" |
| SnpCnvQSet-class | Class "SnpCnvQSet" |
| SnpCopyNumberSet-class | "SnpSet" Extensions |
| SnpCopyNumberSet-methods | "SnpSet" Extensions |
| SnpFeatureSet-class | "FeatureSet" Extensions |
| SnpLevelSet-class | Class "SnpLevelSet" |
| SNPPDInfo-class | Classes "PDInfo" and "SNPPDInfo" |
| SnpQSet-class | Class "SnpQSet" |
| TilingFeatureSet-class | "FeatureSet" Extensions |
| TilingPDInfo-class | Classes "PDInfo" and "SNPPDInfo" |