basejump 0.6.0 (2018-07-17)

Major changes

  • Now importing SummarizedExperiment package and providing basic method support for generics that were previously used in the bcbioBase package.
  • Improved GFFv3 handling in makeGRangesFromGFF and other GFF utility functions, including makeGene2symbolFromGFF and makeTx2geneFromGFF. Note that makeGRangesFromGFF now returns additional metadata columns accessible with S4Vectors::mcols, and that these columns are now sorted alphabetically.

Migrated functions

Previously, these functions were exported in the bcbioBase package, but they provide non-bcbio-specific functionality, and should be included here in the basejump package instead:

  • assertFormalInterestingGroups.
  • gene2symbol.
  • interestingGroups, uniteInterestingGroups.
  • sampleData, sanitizeSampleData.
  • sampleNames.
  • selectSamples.

Providing basic SummarizedExperiment class method support for counts.

Minor changes

  • geometricMean generic was not exported correctly.

basejump 0.6.1 (2018-07-21)

Minor changes

  • Bug fix for convertGenesToSymbols method for SummarizedExperiment. Previously, if geneName column was a factor, this function would error. This issue has been fixed by ensuring that the symbols provided in geneName are coerced to a character vector.
  • Improved conda installation instructions.

basejump 0.6.2 (2018-07-31)

New functions

  • convertSymbolsToGenes: provides SummarizedExperiment method support for converting objects containing gene symbols (“geneName”) as rownames back to gene identifiers (“geneID”).
  • eggnog: quickly download current annotations from EggNOG database. Useful for annotating gene-to-protein matches; currently in use with the brightworm RNAi screening package, which contains WormBase gene ID and EggNOG ID annotations.

Major changes

  • Now suggesting BiocManager instead of BiocInstaller for installation.
  • broadClass now supports GRanges and SummarizedExperiment. Support for data.frame and/or DataFrame class objects has been removed.

Minor changes

  • convertGenesToSymbols and convertTranscriptsToGenes now have organism and gene2symbol arguments set NULL by default.
  • Upgraded to roxygen2 v6.1 for documentation, which improves handling of aliases in the Rd manual files.
  • Added dplyr::pull to reexported functions.
  • Improved package documentation by declaring the supported class(es) for each function argument.
  • Moved foldChangeToLogRatio and logRatioToFoldChange constructors into numeric method declarations.
  • Simplified internal code for gene2symbol SummarizedExperiment method.
  • toStringUnique now uses x instead of atomic as primary argument.

basejump 0.6.3 (2018-08-01)

Minor changes

  • Migrated separatorBar and updateMessage global export from bcbioBase. Improved separatorBar appeareance to automatically scale to current session width, using getOption("width").

basejump 0.6.4 (2018-08-03)

New functions

  • matchInterestingGroups: New developer function to automatically handle interestingGroups argument used across various plotting functions and in the bcbio infrastructure packges.