## 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

