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Version 0.3

AcidExperiment 0.3.0 (2022-03-11)

Major changes:

  • export: Reworked SummarizedExperiment to use new BiocIO generic approach. This generic now uses con instead of dir to define the directory path. Note that previously, the object name would be defined as a subdirectory when using dir to define the path. We are currently keeping this legacy approach when using dir, but no attempt to parse the object name and create a corresponding subdirectory is employed when using the new con argument.
  • convertGenesToSymbols and convertSymbolsToGenes: Simplified the number of exported methods to now simply dispatch on SummarizedExperiment. Added support for new strict mode check, which intentionally does not allow propagation of any NA values during interconversion steps.

Minor changes:

  • selectSamples: The function now automatically relevels factors defined in colData.
  • Reworked internal code to no longer depend on formalsList and getNameInParent from AcidBase package. Note that getNameInParent is now only exported in goalie package. Also removed import of now defunct as.data.frame methods previously defined in pipette package.
  • S4 methods are now defined alphabetically in package documentation.
  • Hardened internal mapGenes code to no longer use tryCatch call and silently error on map failure.
  • selectSamples: Factors defined in colData are now automatically releveled via internal droplevels call for SummarizedExperiment method.