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| $,ParESet-method | Class "ParESet" |
| $<-,ParESet-method | Class "ParESet" |
| addFeatureData | Method for Function addFeatureData |
| addFeatureData,eSet-method | Method for Function addFeatureData |
| addFeatureData-methods | Method for Function addFeatureData |
| alleleA | Accessor for the A allele |
| alleleA,AnnotatedDataFrame-method | Accessor for the A allele |
| alleleA,SnpLevelSet-method | Accessor for the A allele |
| alleleB | Accessor for the B allele |
| alleleB,AnnotatedDataFrame-method | Accessor for the B allele |
| alleleB,SnpLevelSet-method | Accessor for the B allele |
| allPlots | Extracts graphical parameters to be used by all plotting devices |
| allPlots,ParESet-method | Class "ParESet" |
| AnnotatedSnpCallSet-class | Deprecated classes |
| AnnotatedSnpCopyNumberSet-class | Deprecated classes |
| AnnotatedSnpSet-class | Deprecated classes |
| calculateCopyNumber | Extracts copy number estimates from thetas in SnpQSet object |
| calculateCopyNumber,SnpQSet-method | Extracts copy number estimates from thetas in SnpQSet object |
| calculateCopyNumber-methods | Extracts copy number estimates from thetas in SnpQSet object |
| centromere | Coordinates of centromere |
| chromosome | Accessor for chromosome SNP annotation |
| chromosome,AnnotatedDataFrame-method | Accessor for chromosome SNP annotation |
| chromosome,SnpLevelSet-method | Accessor for chromosome SNP annotation |
| chromosome-methods | Accessor for chromosome SNP annotation |
| chromosomeAnnotation | chromosome annotation |
| chromosomeSize | Get size of chromosome in number of base pairs. |
| coerce,AnnotatedSnpCallSet,SnpCallSet-method | Methods for Function coerce |
| coerce,AnnotatedSnpCopyNumberSet,SnpCopyNumberSet-method | Methods for Function coerce |
| coerce,AnnotatedSnpSet,oligoSnpSet-method | Methods for Function coerce |
| coerce-methods | Methods for Function coerce |
| cytoband | Start and stop sites of cytoband |
| dbSnpId | The dbSNP identifier |
| dbSnpId,AnnotatedDataFrame-method | The dbSNP identifier |
| dbSnpId,SnpLevelSet-method | The dbSNP identifier |
| enzyme | Enzyme used to digest DNA |
| enzyme,AnnotatedDataFrame-method | Enzyme used to digest DNA |
| enzyme,SnpLevelSet-method | Enzyme used to digest DNA |
| fragmentLength | Accessor for the fragment length |
| fragmentLength,AnnotatedDataFrame-method | Accessor for the fragment length |
| fragmentLength,SnpLevelSet-method | Accessor for the fragment length |
| getPar | Computes default graphical parameters |
| getPar,SnpLevelSet-method | Computes default graphical parameters |
| getPar-methods | Computes default graphical parameters |
| getSnpAnnotation | Retrieves SNP-level annotation |
| getSnpAnnotation,oligoSnpSet-method | Retrieves SNP-level annotation |
| getSnpAnnotation,SnpCallSet-method | Retrieves SNP-level annotation |
| getSnpAnnotation,SnpCopyNumberSet-method | Retrieves SNP-level annotation |
| getSnpAnnotation,SnpLevelSet-method | Retrieves SNP-level annotation |
| hapmap | Data from the hapmap project |
| initialize,oligoSnpSet-method | Generates instances of SnpSet objects |
| initialize,ParESet-method | Class "ParESet" |
| initialize,ParSnpCallSet-method | Class "ParSnpCallSet" |
| initialize,ParSnpCopyNumberSet-method | Class "ParSnpCopyNumberSet" |
| initialize,ParSnpSet-method | Class "ParSnpSet" |
| initialize-methods | Generates instances of SnpSet objects |
| ParESet-class | Class "ParESet" |
| ParSnpCallSet-class | Class "ParSnpCallSet" |
| ParSnpCopyNumberSet-class | Class "ParSnpCopyNumberSet" |
| ParSnpSet-class | Class "ParSnpSet" |
| plotCytoband | Plots cytoband for one chromosome |
| plotSnp | Plots copy number and genotype calls against physical position |
| plotSnp,ParESet,ANY-method | Plots copy number and genotype calls against physical position |
| plotSnp,ParSnpCallSet,SnpCallSet-method | Plots copy number and genotype calls against physical position |
| plotSnp,ParSnpCopyNumberSet,SnpCopyNumberSet-method | Plots copy number and genotype calls against physical position |
| plotSnp,ParSnpSet,oligoSnpSet-method | Plots copy number and genotype calls against physical position |
| position | Physical position of SNP on chromosome |
| position,AnnotatedDataFrame-method | Physical position of SNP on chromosome |
| position,SnpLevelSet-method | Physical position of SNP on chromosome |
| sample.snpset | Example object of class oligoSnpSet |
| selectSomeIndex | Method from Biobase for selecting indices |
| selectSomeIndex,data.frame-method | Method from Biobase for selecting indices |
| show,oligoSnpSet-method | show methods |
| show-methods | show methods |
| showSummary | Displays descriptive statistics for a sample. |
| smoothSnp | A simple nonparametric smoother for genotype and copy number |
| smoothSnp,oligoSnpSet-method | A simple nonparametric smoother for genotype and copy number |
| snpPar | Accessor for graphical parameters |
| snpPar,ParESet-method | Class "ParESet" |
| snpPar<-,ParESet-method | Class "ParESet" |
| summary,AnnotatedSnpSet-method | Methods for Function summary |
| summary,ANY-method | Methods for Function summary |
| summary,oligoSnpSet-method | Methods for Function summary |
| summary,SnpCallSet-method | Methods for Function summary |
| summary-methods | Methods for Function summary |
| unsplitSnpSet | Combines a list with elements that are AnnotatedSnpSets into one AnnotatedSnpSet. |
| unsplitSnpSet,list,AnnotatedDataFrame-method | Combines a list with elements that are AnnotatedSnpSets into one AnnotatedSnpSet. |
| unsplitSnpSet-methods | Combines a list with elements that are AnnotatedSnpSets into one AnnotatedSnpSet. |
| updateObject,AnnotatedSnpSet-method | updateObject methods |
| updateObject,oligoSnpSet-method | updateObject methods |