basejump 0.7.0 (2018-08-07)

In this release, we are migrating some of the S4 generics previously exported in the bcbioBase package. We are consolidating these functions here for simplicity and stability.

New functions

  • makeSummarizedExperiment: Renamed prepareSummarizedExperiment, previously exported in the bcbioBase package. We are using the make prefix here for consistency (see other gene annotation functions).
  • Migrated S4 generics and methods from bcbioBase: flatFiles, metrics, plotCorrleationHeatmap, plotGene, plotHeatmap, plotQC, and plotQuantileHeatmap.

Major changes

  • Now using curl::has_internet internally to check for Internet connection. This applies to the annotation functions that query web databases.
  • Added coercion method support for converting a SummarizedExperiment to an unstructured list. This is the method used internally for flatFiles.

basejump 0.7.1 (2018-08-18)

New functions

  • cleanSystemLibrary: Utility function to check whether a user has installed packages into the R system library. Refer to .libPaths documentation for more information on library paths.

Major changes

  • Now using build instead of genomeBuild for Ensembl annotation functions. The genomeBuild argument still works but now will inform the user about the change.

Minor changes

  • Migrated prepareTemplate from bcbioBase package. Simplifed this function to copy all files inside extdata/rmarkdown/shared within a specified package. Currently in use for bcbioRNASeq, bcbioSingleCell, and the new pointillism clustering package.
  • Made Ensembl release matching stricter, based on the metadata columns.

basejump 0.7.2 (2018-08-29)

New functions

  • assertAllAreURL.
  • assertAllAreValidNames.
  • validNames.

Major changes

  • Added a draft vignette explaining the functions available in the package.
  • gene2symbol, makeGene2symbolFromEnsembl, and makeGene2symbolFromGFF functions now support the unique argument, which returns sanitized values in the geneName column, ensuring there are no duplicates. This is enabled by default (recommended) but can be disabled using unique = FALSE. This functionality was added to ensure consistent gene name handling in single-cell RNA-seq analyses.
  • saveData now supports basejump.save.ext and basejump.save.compress global options, so the desired file type (e.g. RDS instead of RDA) and compression (e.g. xz instead of gzip) can be easily specified for an entire project.

Minor changes

  • sampleNames now supports assignment for SummarizedExperiment method.
  • Now exporting lanePattern regular expression pattern as a global, which was previously defined in the bcbioBase package.
  • Bug fix for as coercion method support. Need to ensure exportMethods(coerce) is included in NAMESPACE file, otherwise tibble coercion using as(x, "tbl_df") won’t work when called from an Rscript without the package library loaded. Thanks @roryk for noticing this.
  • Updated gene2symbol generic to use ..., since we’ve added the unique = TRUE argument in this release.
  • annotable: Moved to makeGRanges.R file, and improved the internal code to export supported formals also used in makeGRangesFromEnsembl. The function should work exactly the same as previous releases, but now with clearer supported arguments in the documentation.
  • Skipping code coverage for cleanSystemLibrary, since Travis CI installs packages into the system library, and causes this check to return FALSE.
  • Consistently using as(from, "tbl_df") for internal tibble coercion in all functions.
  • geneSynonyms and panther: organism argument matching no longer suggests a default. The current list of supported organisms is in the documentation, and described in the internal match.arg call.
  • All SummarizedExperiment methods use validObject validity checks, where applicable.
  • Consolidated documentation for all makeGRanges, makeGene2symbol, and makeTx2gene functions.
  • Heatmap functions: simplified the internal code responsible for defining annotationCol and annotationColors automatically.
  • sampleData: Made validity check stricter, requiring sampleName column to be defined, otherwise the function will intentionally error.
  • Now using formals internall to keep ggplot2 theme formals consistent.
  • Updated example data scripts and resaved internal data.
  • Updated contribution guidelines in CONTRIBUTING.md file.