bcbioBase 0.2.14 (2018-05-18)

Minor changes

  • Improved formatting of package NEWS
  • Improved code coverage by adding ggplot2 unit testing.
  • Added sampleData<- method support for standard data.frame.

bcbioBase 0.2.13 (2018-05-07)

Minor changes

  • Added overwrite parameter to prepareTemplate(), disabled by default.
  • Removed validity check for sampleData() accessor.
  • Improved vector return in sampleNames().

bcbioBase 0.2.12 (2018-05-08)

Minor changes

  • Migrated sanitizeSampleData() from basejump to bcbioBase.
  • Don’t return interestingGroups column in sampleData() return when clean = TRUE.
  • Removed internal R Markdown shared files. These are already saved per bcbio R package.

bcbioBase 0.2.11 (2018-05-07)

New methods

  • Added SummarizedExperiment method support for sampleNames() generic.

bcbioBase 0.2.10 (2018-05-03)

New functions

bcbioBase 0.2.9 (2018-04-30)

Minor changes

  • Improved assert check messages for interesting groups.
  • Switched back to internally using make.unique() instead of make.names() for convertGenesToSymbols() coercion on SummarizedExperiment objects. We’re using make.names() only when coercing seurat objects (see [bcbioSingleCell][] code).
  • Updated RangedSummarizedExperiment working example, based on bcbioRNASeq example dataset.

bcbioBase 0.2.8 (2018-04-25)

Minor changes

  • Split out assertive imports so we can pin release to bioconda.

bcbioBase 0.2.7 (2018-04-25)

Minor changes

  • Updated recommended Bioconductor installation method for 3.7 release.
  • Attempt to add description to metadataBlacklist.
  • readSampleData(): Use description metadata column internally instead of sampleID.

bcbioBase 0.2.6 (2018-04-25)

Minor changes

bcbioBase 0.2.5 (2018-04-24)

Major changes

  • sampleData() now supports clean = TRUE argument, which will hide columns that contain metrics or other calculations from the user. This is useful when preparing an R Markdown report, where we only want to show relevant metadata (e.g. factor columns). This is enabled by default.
  • Now using metadataBlacklist to hide specific columns in sample metadata.
  • sampleMetadata() is now deprecated in favor of sampleData(). This function still works but will now warn the user, and should be removed from R Markdown template code.
  • Added SummarizedExperiment to list coercion support, which uses the same code as flatFiles().
  • readSampleData() no longer requires or recommended fileName column. Only the description column is required for demultiplexed data. In the case of multiplexed samples (e.g. inDrops single-cell RNA-seq), then sampleName, index and sequence names are also required. Multiplexed cell ranger data only requires sampleName and index, since the index barcode isn’t present in the counts matrix.

Minor changes

  • sampleID is no longer included in metadata priority columns. This is only to be used internally and should be hidden from the user where possible.
  • prepareSampleData() is no longer needed and is now defunct.

bcbioBase 0.2.4 (2018-04-22)

Minor changes

  • Reworked internal code for readYAML() family of functions.
  • Reorganized and improved default arguments for heatmap functions.
  • readSampleData(): switched to using merge() instead of left_join() internally.
  • Reexporting viridis family of color functions, including inferno(), and the British variant scale_colour_viridis().

bcbioBase 0.2.3 (2018-04-19)

  • plotHeatmap(), plotQuantileHeatmap(): Always attempt to convert genes to symbols for heatmaps.

bcbioBase 0.2.2 (2018-04-16)

Minor changes

bcbioBase 0.2.1 (2018-04-13)

Major changes

  • convertGenesToSymbols() now has method support for SummarizedExperiment.
  • Updated example datasets to use rse_bcb and rse_dds.
  • Simplified internal S4 method code for heatmap functions.
  • prepareSummarizedExperiment() now supports transgenes with the transgeneNames argument (e.g. “EGFP”), and FASTA spike-ins with the spikeNames argument (e.g. “ERCCs”). Additionally, rowRanges and colData are no longer required and can be left NULL, although this isn’t generally recommended.

Minor changes

  • Consolidated sampleYAML() function code.
  • Consolidated assert check imports into bcbioBase-package.R file.
  • Consolidated globals into globals.R file.
  • Improved internal pheatmap color support.

bcbioBase 0.2.0 (2018-03-22)

Major changes

  • Added sampleData() generic. Providing method support for SummarizedExperiment class. This generic provides consistent sample metadata support in both the [bcbioRNASeq][] and [bcbioSingleCell][] packages. For [bcbioSingleCell][], colData() returns information about the cells, not the samples. For [bcbioRNASeq][], colData() and sampleData() provide similar information on the samples.
  • Added uniteInterestingGroups() as a generic. Provides support for adding an interestingGroups column to a data frame.
  • Added SummarizedExperiment method support for gene2symbol(), interestingGroups() generics.
  • Converted prepareSummarizedExperiment() from a generic to a standard function.
  • prepareSummarizedExperiment() now requires rowRanges and supports FASTA spike-ins with isSpike argument. This helps set up a SingleCellExperiment object in the [bcbioSingleCell][] package.
  • prepareTemplate() has been converted from a generic to a standard function.
  • readDataVersions() and readProgramVersions() now return an empty tibble if the file is missing. bcbio doesn’t always output these files, so we have changed the behavior from stopping on a missing file to simply warning and returning empty.
  • Added sampleDirs() function, that informs the user about the names of the sample directories in the bcbio run.

Minor changes

  • Improved internal factor sanitization of sample metadata for readSampleMetadataFile() and sampleYAMLMetadata().
  • Exporting projectDirPattern to match bcbio project directories (e.g. 2018-01-01_rnaseq) across packages.
  • Changed default of rdsToken in copyToDropbox() to be NULL instead of NA.
  • Reduced the number of imports from basejump package.
  • Now using sessioninfo::session_info() instead of devtools::session_info().
  • Added AppVeyor CI support for code testing on Windows.
  • Made Travis CI checking stricter and added BiocCheck().
  • Simplified package dependencies in DESCRIPTION.

Deprecations

bcbioBase 0.1.4 (2018-02-20)

  • Don’t include sample metadata in summaryYAMLMetrics() return.

bcbioBase 0.1.3 (2018-02-19)

bcbioBase 0.1.2 (2018-02-18)

bcbioBase 0.1.1 (2018-02-17)

  • Added internal assert checks.
  • Now exporting sampleMetadata<-() assignment generic.
  • Updated encrypted token for rdrop2 working example.
  • Added assert_formal_interesting_groups() assert checks. Deprecated checkInterestingGroups().

bcbioBase 0.1.0 (2018-02-13)

  • Preparing version pinning for bioconda. Relaxed rlang dependency from v0.1.6 to v0.1.2 and tidyr dependency from v0.7.2 to v0.7.1.
  • Added copyToDropbox() function, which enables input of a list of local files and returns Dropbox paths using rdrop2.
  • Updated basejump dependency to v0.2.1.
  • Added assertive checks for all functions.

bcbioBase 0.0.3 (2018-01-27)

  • NAMESPACE export fixes.
  • Minor code cleanup to pass lintr checks.
  • Switched to rlang methods for errors, messages, and warnings: abort(), inform(), and warn().
  • Messages now consistently use backticks instead of apostrophes, as recommended by the tidyverse style guide.
  • Removed tibble rownames support from prepareSampleMetadata().
  • Improved code coverage to 100%.

bcbioBase 0.0.2 (2018-01-19)

  • Re-export assignAndSaveData(), loadData(), loadRemoteData(), saveData() from basejump package.
  • Update prepareTemplate() function to use internally stored data.

bcbioBase 0.0.1 (2018-01-11)

  • Initial release.