basejump 0.4.0 (2018-03-22)

Major changes

  • Introducing new functions for the acquistion of gene and transcript annotations from Ensembl: ensembl, genes, and transcripts. These functions allow the return of GRanges, DataFrame, and data.frame class objects from AnnotationHub using ensembldb.
  • Improved internal broadClass definition code to match against chromosome from Ensembl if available.
  • loadDataAsName now works with unquoted names, improving consistency with loadData (non-standard evaluation).

Minor changes

  • Added new convertUCSCBuildToEnsembl function, for easy remapping of UCSC to Ensembl genome build names (e.g. hg38 to GRCh38).
  • Migrated matrix methods for plotCorrelationHeatmap here from bcbioRNASeq, for improved consistency with other heatmap functions.
  • Exporting makeNames variant of base::make.names that sanitizes using underscores rather than dots.
  • Converted readYAML from a generic to standard function.
  • Added support for AppVeyor CI code testing on Windows.
  • Made Travis CI build checks stricter, adding support for BiocCheck.
  • Added new assert checks: assertAreGeneAnnotations, assertAreTranscriptAnnotations, isAnImplicitInteger.
  • Simplified working examples for assert checks to just show successes.

Deprecations

  • annotable function has been deprecated in favor of the new ensembl function.
  • checkAnnotable deprecated in favor of assertIsAnnotable.
  • checkGene2symbol deprecated in favor of assertIsGene2symbol.
  • checkTx2gene deprecated in favor of assertIsTx2gene.
  • assertFormalColorFunction deprecated in favor of assertIsHexColorFunctionOrNULL.
  • initializeDir deprecated in favor of initializeDirectory.
  • Defunct: summarizeRows, wash, packageSE, prepareSE, metadataTable, comp, revcomp, symbol2gene.