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| crlmm-package | Genotype Calling via CRLMM Algorithm |
| $,CrlmmSetList-method | Class "CrlmmSetList" |
| A | Class "ABset" |
| A,ABset-method | Class "ABset" |
| A,CrlmmSetList-method | Class "CrlmmSetList" |
| A<- | Class "CrlmmSetList" |
| A<-,ABset,matrix-method | Class "ABset" |
| A<-,CrlmmSetList,matrix-method | Class "CrlmmSetList" |
| ABset-class | Class "ABset" |
| addFeatureAnnotation | Class "CrlmmSetList" |
| addFeatureAnnotation,CrlmmSetList-method | Class "CrlmmSetList" |
| B | Class "ABset" |
| B,ABset-method | Class "ABset" |
| B,CrlmmSetList-method | Class "CrlmmSetList" |
| B<- | Class "CrlmmSetList" |
| B<-,ABset,matrix-method | Class "ABset" |
| B<-,CrlmmSetList,matrix-method | Class "CrlmmSetList" |
| batch | Stores information on the batch (e.g., chemistry plate) used to process samples. |
| batch,CopyNumberSet-method | Class "CopyNumberSet" |
| batch,CrlmmSetList-method | Class "CrlmmSetList" |
| CA | Class "CopyNumberSet" |
| CA,CopyNumberSet-method | Class "CopyNumberSet" |
| CA,CrlmmSetList-method | Class "CrlmmSetList" |
| CA<- | Class "CopyNumberSet" |
| CA<-,CopyNumberSet,matrix-method | Class "CopyNumberSet" |
| CA<-,CrlmmSetList,matrix-method | Class "CrlmmSetList" |
| calls | Accessors for Calls and Confidences on a SnpSet object |
| calls,CrlmmSetList-method | Class "CrlmmSetList" |
| calls,SnpSet-method | Accessors for Calls and Confidences on a SnpSet object |
| CB | Class "CopyNumberSet" |
| CB,CopyNumberSet-method | Class "CopyNumberSet" |
| CB,CrlmmSetList-method | Class "CrlmmSetList" |
| CB<- | Class "CopyNumberSet" |
| CB<-,CopyNumberSet,matrix-method | Class "CopyNumberSet" |
| CB<-,CrlmmSetList,matrix-method | Class "CrlmmSetList" |
| celDates | Extract dates from the cel file header |
| chromosome | Methods for eSet derivatives |
| chromosome,CopyNumberSet-method | Class "CopyNumberSet" |
| chromosome,CrlmmSetList-method | Class "CrlmmSetList" |
| chromosome,eSet-method | Methods for eSet derivatives |
| cnIndex | Methods for eSet derivatives |
| cnIndex,CrlmmSetList-method | Class "CrlmmSetList" |
| cnIndex,eSet-method | Methods for eSet derivatives |
| cnrma | Quantile normalizes the intensities for the nonpolymorphic probe to a HapMap reference distribution. |
| combine,CrlmmSetList,CrlmmSetList-method | Class "CrlmmSetList" |
| computeCopynumber | Computes copy number |
| confs | Accessors for Calls and Confidences on a SnpSet object |
| confs,CrlmmSetList-method | Class "CrlmmSetList" |
| confs,SnpSet-method | Accessors for Calls and Confidences on a SnpSet object |
| copyNumber,CopyNumberSet-method | Class "CopyNumberSet" |
| copyNumber,CrlmmSetList-method | Class "CrlmmSetList" |
| CopyNumberSet-class | Class "CopyNumberSet" |
| crlmm | Genotype oligonucleotide arrays with CRLMM |
| crlmmIllumina | Genotype Illumina Infinium II BeadChip data with CRLMM |
| CrlmmSetList-class | Class "CrlmmSetList" |
| crlmmWrapper | Wrapper to quantile normalize and genotype Affymetrix 6.0 cel files. |
| ellipse,CopyNumberSet-method | Class "CopyNumberSet" |
| list.celfiles | List CEL files. |
| ncol,CrlmmSetList-method | Class "CrlmmSetList" |
| nrow,CrlmmSetList-method | Class "CrlmmSetList" |
| plot,ABset,CopyNumberSet-method | Class "CopyNumberSet" |
| plot,CrlmmSetList,ANY-method | Class "CrlmmSetList" |
| points,CrlmmSetList-method | Class "CrlmmSetList" |
| position | Methods for eSet derivatives |
| position,CopyNumberSet-method | Class "CopyNumberSet" |
| position,CrlmmSetList-method | Class "CrlmmSetList" |
| position,eSet-method | Methods for eSet derivatives |
| readIdatFiles | Reads Idat Files from Infinium II Illumina BeadChips |
| sampleNames,CrlmmSetList-method | Class "CrlmmSetList" |
| show,CrlmmSetList-method | Class "CrlmmSetList" |
| snpIndex | Methods for eSet derivatives |
| snpIndex,CrlmmSetList-method | Class "CrlmmSetList" |
| snpIndex,eSet-method | Methods for eSet derivatives |
| snprma | Preprocessing tool for SNP arrays. |
| update,character-method | Class "CrlmmSetList" |
| update,CrlmmSetList-method | Class "CrlmmSetList" |
| [,CrlmmSetList-method | Class "CrlmmSetList" |