Changes in version 1.28.1 Bug fixes and minor improvements - Ensure order is the same in both sparse and dense outputs of compactAssay (@csoneson, #30) New features - Added citation information to the vignette and package. See citation(package = "RaggedExperiment") Changes in version 1.26.0 New features - Added a contributed vignette for ASCAT workflows (@Lydia-King, #28). Changes in version 1.24.0 Bug fixes and minor improvements - Use full argument names in unit tests. - Invoke colSums from MatrixGenerics in unit tests. Changes in version 1.22.0 New features - Add as.list and as.data.frame methods to RaggedExperiment to facilitate extraction of mcols and conversion to table format, respectively. Changes in version 1.18.0 New features - Sparse matrices of dgCMatrix type can now be coerced to RaggedExperiment when rownames are coercible to GRanges Bug fixes and minor improvements - 'counts' set as the default name for the values in mcols after coercion from dgCMatrix Changes in version 1.16.0 New features - sparseAssay and compactAssay now support sparseMatrix outputs from the Matrix package Changes in version 1.14.0 Bug fixes and minor improvements - Update package to changes in MatrixGenerics (new location of the rowRanges generic) Changes in version 1.12.0 Bug fixes and minor improvements - Adjust to changes from SummarizedExperiment::assay (withDimnames argument) - Reference simplifyTCGA helper function from TCGAutils in examples - Restore original real-world qreduceAssay example and include alternative qreduceTCGA example Changes in version 1.10.0 Bug fixes and minor improvements - Include reference to TCGAutils functions for qreduceAssay examples - Add robustness to RaggedExperiment constructor including unit tests - Include class and assay operations overview schematic in the vignette Changes in version 0.0.24 New features - RaggedExperiment vignette now available. - Submission to Bioconductor/Contributions issue tracker Changes in version 0.0.21 New Features - Software for copy number, mutation, and other ragged array data representations - RaggedExperiment class and basic methods: subsetting, dimnames, etc. - Assay methods expose a particular metadata column and creates a retangular matrix - Coerce functions from RaggedExperiment to SummarizedExperiment class available