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Version 0.1

AcidExperiment 0.1.0 (2021-02-05)

Initial release, with code migrated from basejump package.

AcidExperiment 0.1.1 (2021-02-06)

Major changes:

  • Ensuring we’re enforcing lower camel case naming conventions for metadata describing the columns slotted in colData.

Minor changes:

  • Imported coercion methods from SummarizedExperiment.
  • Added package.R, describing package info.

AcidExperiment 0.1.2 (2021-02-06)

Minor changes:

  • Added ignoreVersion option to gene mapping functions.

AcidExperiment 0.1.3 (2021-02-08)

Minor changes:

  • sampleData: Bug fix for unwanted early return on minimal colData defined in SummarizedExperiment. This handling is required for downstream automatic plotting functions defined in AcidPlots, that make use of “sampleName” metadata column.

AcidExperiment 0.1.4 (2021-02-08)

Minor changes:

  • Now reexporting some commonly used functions from SummarizedExperiment.

AcidExperiment 0.1.5 (2021-02-09)

Minor changes:

  • Reworked the list of reexported functions. Now reexporting only from SummarizedExperiment and sessioninfo.

AcidExperiment 0.1.6 (2021-02-11)

Minor changes:

  • Internal NAMESPACE rework, using pipette and AcidGenerics.

AcidExperiment 0.1.7 (2021-02-13)

Minor changes:

  • More internal NAMESPACE reworks. IRanges classes now defined in AcidGenerics.

AcidExperiment 0.1.8 (2021-02-22)

Minor changes:

  • Now enforcing lower camel case for sampleData return.
  • Simplified generic handling for Matrix methods.

AcidExperiment 0.1.9 (2021-02-25)

Minor changes:

  • Renamed all internal instances of “blacklist” to “denylist”.
  • Added denylist override option to makeSummarizedExperiment (recommended to be left enabled by default), which will be used in cBioPortalAnalysis package update.

AcidExperiment 0.1.10 (2021-03-10)

Minor changes:

  • makeSummarizedExperiment: Relaxed the validity check on syntactically valid names in rownames and colnames of the object. Now the function informs the user with a CLI message instead of erroring.

AcidExperiment 0.1.11 (2021-06-04)

Minor changes:

  • Updated the documentation to provide compatibility with R 4.1 and Bioconductor 3.13 release.
  • Updated dependency versions.

AcidExperiment 0.1.12 (2021-06-10)

Minor changes:

  • mapGenesToRownames, mapGenesToIDs, mapGenesToSymbols: Improved the flexibility of gene identifier matching for SummarizedExperiment method. Now also attempts to match against geneSynonyms when defined in rowData, which is incredibly useful for easy matching of deprecated gene names.
  • Removed unnecessary Gene2Symbol methods for mapGenesToRownames, mapGenesToIDs, and mapGenesToSymbols.
  • matchesGene2Symbol no longer attempts to use the now removed Gene2Symbol method for mapGenesToRownames internally. We simplified this check using the internal .mapGenes function to locate index position instead.

AcidExperiment 0.1.13 (2021-08-09)

Minor changes:

  • Updated package dependency version cutoffs.
  • Gene2Symbol: Tightened up internal match.arg handling for format argument, in defined SummarizedExperiment method.

AcidExperiment 0.1.14 (2021-08-11)

Major changes:

  • convertGenesToSymbols: Added strict and quiet arguments. Improved and hardened internal code, improving the verbosity of calls to Gene2Symbol generator. Added additional asserts to ensure that mismatches (e.g. row flipping) don’t occur.
  • Ensembl2Entrez, Gene2Symbol: Updated formals to passthrough to other primary methods defined in AcidGenomes package.

Minor changes:

  • Hardened and expanded code coverage for expected gene-to-symbol mapping behavior in main Gene2Symbol generator, focusing on the format argument.