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| annotCols | Get annotation columns |
| annotCols<- | Set annotation columns |
| annotRows | Get annotation rows |
| annotRows<- | Set annotation rows |
| as.ExpressionSet.matrixData | Coerces a MatrixData into an ExpressionSet |
| as.matrixData.ExpressionSet | Coerces an ExpressionSet into a MatrixData |
| boolParamValue | Bool parameter value |
| create_annotRows | Create annotation rows |
| description | Get column description |
| description<- | Set column description |
| imputeData | Get imputation of main data frame |
| imputeData<- | Set imputation of main data frame |
| infer_perseus_annotation_types | Infer Perseus type annotation row from DataFrame column classes |
| initialize-method | matrixData initializer |
| intParamValue | Int parameter value |
| main | Get main columns |
| main<- | Set main columns |
| matrixData | matrixData constructor |
| matrixData-class | MatrixData |
| MatrixDataCheck | MatrixDataCheck: a function to check the validity of an object as a perseus data frame |
| MatrixDataCheck.default | MatrixDataCheck: a function to check the validity of an object as a perseus data frame |
| MatrixDataCheck.ExpressionSet | MatrixDataCheck: a function to check the validity of an object as a perseus data frame |
| MatrixDataCheck.list | MatrixDataCheck: a function to check the validity of an object as a perseus data frame |
| MatrixDataCheck.matrixData | MatrixDataCheck: a function to check the validity of an object as a perseus data frame |
| names-method | Get names |
| names.matrixData | Column names of main and annotation columns |
| parseParameters | Parse parameters |
| qualityData | Get quality values of main data frame |
| qualityData<- | Set quality values of main data frame |
| read.perseus | Read Perseus matrix files |
| read.perseus.as.ExpressionSet | Read Perseus matrix files |
| read.perseus.as.list | Read Perseus matrix files |
| read.perseus.as.matrixData | Read Perseus matrix files |
| read.perseus.default | Read Perseus matrix files |
| singleChoiceParamInd | Single choice index |
| singleChoiceParamValue | Single choice value |
| write.perseus | write.perseus: function to generate a perseus-readable text document |
| write.perseus.data.frame | write.perseus: function to generate a perseus-readable text document |
| write.perseus.default | write.perseus: function to generate a perseus-readable text document |
| write.perseus.ExpressionSet | write.perseus: function to generate a perseus-readable text document |
| write.perseus.list | write.perseus: function to generate a perseus-readable text document |
| write.perseus.matrix | write.perseus: function to generate a perseus-readable text document |
| write.perseus.matrixData | write.perseus: function to generate a perseus-readable text document |