basejump 0.2.0 (2018-01-28)

  • Offloaded internal bcbio-specific code to new package named bcbioBase. Consequently, this makes the basejump package leaner, meaner, and easier to manage. The following functions are now exported in that package: bcbio, checkInterestingGroups, flatFiles, interestingGroups, metrics, plotDot, plotGene, plotQC, plotViolin, prepareSummarizedExperiment, prepareTemplate, readDataVersions, readLogFile, readProgramVersions, readSampleMetadataFile, sampleMetadata, sampleYAML, sampleYAMLMetadata, sampleYAMLMetrics, and selectSamples. These functions are now deprecated here in basejump (see deprecated.R file for more information).
  • comp and revcomp have been deprecated in favor of complement and reverseComplement from the Biostrings package.
  • Internally, errors, messages, and warnings now use methods from the rlang package: abort, inform, and warn, in place of stop, message, and warning, respectively.
  • Improved error handing for missing files in loadData. Additionally, the file name must match the internal name in the RData file, otherwise loadData will warn the user. This is more strict than the default behavior of base::load, but helps prevent accidental overwrite in the current working environment.
  • localOrRemoteFile, previously an internal function, is now exported.
  • annotable now uses internal GRCh37 annotations from the annotables package, which is saved in the extdata/ directory internally. Previously, these genome annotations were accessed from lazy loaded data saved in the data/ directory of the package repository.
  • annotables now checks for all packages attached by ensembldb and AnnotationHub and forces detachment at the end of the function call. Otherwise, this can result in the unwanted effect of ensembldb masking other user-loaded functions, such as the tidyverse suite (e.g. dplyr::select).
  • Consistently reformatted code indents to be a multple of 4 spaces, as recommended by Bioconductor.
  • camel now handles delimited numbers a little differently. Previously, delimiters in between numbers (e.g. the commas in “1,000,000”) were stripped. Sometimes this can result in confusing names. For example, if we have a column formatted in dotted case containing a decimal (e.g. “resolution.1.6”), the decimal would be stripped (e.g. “resolution16” in camel). Now, we sanitize a numeric delimiter as a lower case “x” character (e.g. “resolution1x6”). This ensures that numbers containing decimals remain semantically meaningful when sanitized with camel.
  • Internally, gsub (and grepl) calls have been simplified to use the default order of “pattern, replacement, x”.
  • Internally, all implicit integers have been converted to explicit integers, where applicable.

basejump 0.2.1 (2018-02-07)

  • Added convertGenesToSymbols and convertTranscriptsToGenes functions. Previously some of this functionality was contained within the gene2symbol and tx2gene generics for the character method. This behavior was inconsistent with gene2symbol and tx2gene usage in the bcbio R packages, so I decided to split these out into separate functions. Now gene2symbol and tx2gene work consistently with the annotable function to return gene-to-symbol and transcript-to-gene identifier mappings in a data.frame.
  • markdownHeader, markdownList, and markdownPlotlist are now exported as S4 generics. The md* function variants are now exported as aliases.
  • geomean has been renamed to geometricMean.
  • Miscellaneous improvements to error messages and warnings.