MatrixDataCheck         MatrixDataCheck: a function to check the
                        validity of an object as a perseus data frame
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,matrixData-method
                        matrixData initializer
intParamValue           Int parameter value
main                    Get main columns
main<-                  Set main columns
matrixData              matrixData constructor
matrixData-class        MatrixData
names,matrixData-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.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
