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