NEWS

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RaggedExperiment 1.34.0

Bug fixes and minor improvements

• Added vignette chunk labels to both vignettes for easier debugging.

RaggedExperiment 1.32.0

Bug fixes and minor improvements

• Added package anchors to links in documentation

RaggedExperiment 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)

RaggedExperiment 1.28.0

New features

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

RaggedExperiment 1.26.0

New features

• Added a contributed vignette for ASCAT workflows (@Lydia-King, #28).

RaggedExperiment 1.24.0

Bug fixes and minor improvements

• Use full argument names in unit tests.
• Invoke colSums from MatrixGenerics in unit tests.

RaggedExperiment 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.

RaggedExperiment 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

RaggedExperiment 1.16.0

New features

• sparseAssay and compactAssay now support sparseMatrix outputs from the Matrix package

RaggedExperiment 1.14.0

Bug fixes and minor improvements

• Update package to changes in MatrixGenerics (new location of the rowRanges generic)

RaggedExperiment 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

RaggedExperiment 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

RaggedExperiment 0.0.24

New features

• RaggedExperiment vignette now available.
• Submission to Bioconductor/Contributions issue tracker

RaggedExperiment 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