metadataargument added toRaggedExperimentconstructor function (@LiNk-NY).
- Ensure order is the same in both sparse and dense outputs of
compactAssay(@csoneson, #30)
- Added citation information to the vignette and package. See
citation(package = "RaggedExperiment")
- Added a contributed vignette for ASCAT workflows (@Lydia-King, #28).
- Use full argument names in unit tests.
- Invoke
colSumsfromMatrixGenericsin unit tests.
- Add
as.listandas.data.framemethods toRaggedExperimentto facilitate extraction ofmcolsand conversion to table format, respectively.
- Sparse matrices of
dgCMatrixtype can now be coerced toRaggedExperimentwhenrownamesare coercible toGRanges
- 'counts' set as the default name for the values in
mcolsafter coercion fromdgCMatrix
sparseAssayandcompactAssaynow supportsparseMatrixoutputs from theMatrixpackage
- Update package to changes in
MatrixGenerics(new location of therowRangesgeneric)
- Adjust to changes from
SummarizedExperiment::assay(withDimnamesargument) - Reference
simplifyTCGAhelper function fromTCGAutilsin examples - Restore original real-world
qreduceAssayexample and include alternativeqreduceTCGAexample
- Include reference to
TCGAutilsfunctions forqreduceAssayexamples - Add robustness to
RaggedExperimentconstructor including unit tests - Include class and assay operations overview schematic in the vignette
RaggedExperimentvignette now available.- Submission to
Bioconductor/Contributionsissue tracker
- Software for copy number, mutation, and other ragged array data representations
RaggedExperimentclass and basic methods: subsetting, dimnames, etc.- Assay methods expose a particular metadata column and creates a retangular matrix
- Coerce functions from
RaggedExperimenttoSummarizedExperimentclass available