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Changelog

Source: NEWS.md

Changes in version 1.32.0

Bug fixes and minor improvements

  • Added package anchors to links in documentation

Changes in version 1.30.0

New features

  • metadata argument added to RaggedExperiment constructor function (@LiNk-NY).

Bug fixes and minor improvements

  • Ensure order is the same in both sparse and dense outputs of compactAssay (@csoneson, #30)

Changes in version 1.28.0

New features

  • Added citation information to the vignette and package. See citation(package = "RaggedExperiment")

Changes in version 1.26.0

New features

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