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Version 0.2

AcidExperiment 0.2.0 (2021-09-03)

Major changes:

  • Reworked and improved unit tests to achieve 100% code coverage.
  • calculateMetrics: Simplifed internal assert checks. The matrix and Matrix methods (handed off from SummarizedExperiment method) now work primarily on rowData instead of rowRanges, since we’re not using any genomic coordinates here in checks. Prefiltering (disabled by default, but can be enabled with prefilter = TRUE) now removes column elements (e.g. cells and/or samples) with all mito counts (mitoRatio >= 1) and an artifically high log10FeaturesPerCount >= 1 value. These settings help make 100% code coverage possible on minimal test datasets.
  • makeSummarizedExperiment: Improved and fixed CLI messages on detected of mismatched features to be slotted into rowRanges. This can happen when incorrect values are defined in ensemblRelease or gffFile. This should help resolve the cryptic CLI error message seen in bcbioRNASeq issue #170.

Minor changes:

  • Made unused matchesGene2Symbol and matchesInterestingGroups functions defunct. These are still reexported in basejump and DESeqAnalysis, which will be cleaned up in future releases.
  • Improved and hardened CLI messages. Now using abort instead of stop internally, to support better stylized error messages.
  • Now calling toStringInline instead of base toString internally to properly handle string handoff to cli package.
  • autopadZeros: SummarizedExperiment method now has sampleNames argument, which allows the user to selectively pad the sample names column sampleNames defined in colData. Enabled by default, matching previous internal behavior.
  • estimateSizeFactors: Simplified internal assert checks that look for any zero libSizes. Also improved code coverage to check for specific values returned by type argument.

AcidExperiment 0.2.1 (2021-09-08)

Minor changes:

  • Now importing bapply from goalie instead of AcidBase.
  • Updated internal gene mapping code to better handle mismatched Gene2Symbol input, which can happen in pointillism package.

AcidExperiment 0.2.2 (2021-09-13)

Major changes:

  • aggregate: Added support via MARGIN argument to work either row-wise (1; default) or column-wise (2). SummarizedExperiment method has been updated to support these conventions. Corresponding aggregateCols and aggregateRows functions have been simplified to merely wrap an aggregate call with MARGIN argument predefined.
  • convertTranscriptsToGenes: Now all assays are aggregated, rather than simplify returning primary counts assay.

Minor changes:

  • calculateMetrics: Updated to support assay argument.
  • convertGenesToSymbols: Removed unnecessary strict argument for SummarizedExperiment method, and simplified handling of mismatched Gene2Symbol internally.
  • estimateSizeFactors now supports assay argument.
  • integerCounts now supports assay argument.
  • aggregate keeps track of mapping factor used internally for SummarizedExperiment method. This is defined as aggregateRows or aggregateCols in the object metadata.