Classes for high-throughput SNP arrays


[Package List] [Top]

Documentation for package ‘oligoClasses’ version 1.4.0

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

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
initialize,SnpQSet-method Class "SnpQSet"
initialize,TilingQSet-method Class "TilingQSet"
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"
TilingQSet-class Class "TilingQSet"