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Version 0.1

DESeqAnalysis 0.1.0 (2018-11-19)

Initial release. Some of the functions defined in this package have been migrated from my bcbioRNASeq R package.

DESeqAnalysis 0.1.1 (2018-12-01)

Major changes:

  • Improved show method for DESeqResultsTables class.

Minor changes:

  • Miscellaneous documentation and working example improvements.
  • Initial set up of testthat unit tests.
  • Added lintr check support.
  • Enabled Travis CI and AppVeyor CI build checks.
  • Added CI badges to README.

DESeqAnalysis 0.1.2 (2018-12-12)

New functions:

  • contrastSamples: Experimental. Return the samples used to generate a corresponding DESeqResults object. May revise this approach to simply store the sample names directly in the DESeqResults in the future.
  • deg: Utility function to obtain DEG gene vector.
  • resultsTables: Migrated from bcbioRNASeq. Enables easy output of directional DEG tables from DESeqResults object.

Major changes:

  • Added new .matchResults internal utility to match DESeqResults.
  • Reworked internal code for export.
  • Removed DESeqResultsTables class.
  • No longer exporting DESeqResults method for plotDEGHeatmap, plotDEGPCA. May add this back in a future release to maintain compatibility with bcbioRNASeq workflow paper.

Minor changes:

  • Miscellaneous documentation and assert check (using goalie) fixes.
  • Improved internal S4 validity checks using goalie::validate instead of assertthat::validate_that.
  • Updated example DESeqAnalysis S4 data set (deseq).
  • Reorganized and improved unit tests.
  • Added a placeholder for updateObject, which must be added in future update.

DESeqAnalysis 0.1.3 (2018-12-13)

Major changes:

  • No longer using results = 1L by default in DESeqAnalysis methods for functions that support pulling a DESeqResults object. This can result in unwanted behavior, and we shouldn’t assume use of first slotted contrast. Now the user must request the desired contrast explicitly.

Minor changes:

  • Improved internal code for plotDEGHeatmap, plotDEGPCA,
  • Code cleanup to pass lintr checks.
  • Miscellaneous documentation (primarily working example) improvements.

DESeqAnalysis 0.1.4 (2019-01-08)

Major changes:

  • Added new R Markdown template designed for a DESeqAnalysis object.

Minor changes:

  • Switched to reexporting generics from bioverbs instead of basejump, where applicable. For example, moved contrastSamples and resultsTables generics (verbs) to bioverbs.
  • Removed internal validateS4 code, instead relying upon goalie::validate.
  • Simplified Travis CI configuration to only test against bioc-release.
  • Simplified internal asserts using nullOK = TRUE, where applicable. This was added in the corresponding release update to goalie.
  • Now using isAlpha instead of containsAlpha for assert check.
  • Split out NAMESPACE imports into a separate imports.R file.

DESeqAnalysis 0.1.5 (2019-01-14)

Major changes:

  • Importing DataFrame to tbl_df coercion methods directly from basejump instead of the transformer package. Note that S4Transfomer package was renamed simply to transformer at this date.

Minor changes:

  • Improved documentation for DESeqAnalysis-class and the corresponding generator function. Refer to the roxygen syntax (e.g. rdname) on how to accomplish this, since it is useful across packages that define S4 class.
  • Improved working examples and removed todo/fixme comments.
  • Tightened up Travis CI and AppVeyor CI config, which now only checks against master branch (e.g. for pull requests). This reduces the overall CI burden, so that pushes to develop branch don’t trigger CI builds.

DESeqAnalysis 0.1.6 (2019-01-23)

Minor changes:

  • Finish requiring results argument for all DESeqAnalysis methods, where applicable. For example, refer to contrastSamples in this release.
  • Removed sanitizeRowData from imports.
  • Draft update to internal .matchResults assert check, looking for missing results argument.

DESeqAnalysis 0.1.7 (2019-01-31)

Minor changes:

  • contrastSamples: Improved internal sample and contrast name handling. No longer attempting to force snake case formatting.
  • Pinned lintr check package to steinbaugh fork.

DESeqAnalysis 0.1.8 (2019-02-08)

This release reworks the S4 class structure and adds DESeqAnalysisList. Note that objects previously saved prior to the v0.1.8 release will no longer return valid when checked using validObject. They can be updated using updateObject.

New classes:

  • DESeqAnalysisList: extends SimpleList, and enables saving of multiple analyses (e.g. per patient clinical data) in a single object. This class makes it much easier to report on multiple complex contrasts.

Major changes:

  • DESeqAnalysis now inherits from Annotated class. This enables support for metadata slot, which can be used to store package version.
  • Improved checks in DESeqAnalysis validity method.

Minor changes:

  • Added support for plotCounts generic, in favor of now deprecated plotGene.
  • Added support for results and resultsNames generics.
  • Added internal code to check lfcShrink type (e.g. apeglm).
  • Added sampleData method support for DESeqAnalysis, thereby simplying the sample_data chunk in differential expression R Markdown template.
  • Updated and improved show method for DESeqAnalysis. This now will return the version of DESeqAnalysis and not just DESeq2.
  • Updated deseq example object.

DESeqAnalysis 0.1.9 (2019-02-12)

Minor changes:

  • R 3.4 compatibility fix for resultsTables, which needs to assign rownames on rowData return.

DESeqAnalysis 0.1.10 (2019-02-18)

Major changes:

  • plotDEGHeatmap, plotDEGPCA: Reworked internal code to export DESeqResults method that maintains backward compatibility with approach used in bcbioRNASeq F1000 paper.
  • Exported additional legacy DESeqResults method support for plotMA, plotVolcano, resultsTables, and topTables, to maintain backward compatibility with bcbioRNASeq R package.

Minor changes:

  • Updated NEWS to include information on all previous releases.

DESeqAnalysis 0.1.11 (2019-03-11)

Minor changes:

  • plotCounts: Removed DESeqDataSet method support, which is now covered inside SummarizedExperiment method support in basejump.
  • Updated differential expression R Markdown template to improve parameterization support.

DESeqAnalysis 0.1.12 (2019-03-18)

Minor changes:

  • Updated differential expression template and dependencies.

DESeqAnalysis 0.1.13 (2019-03-23)

Minor changes:

DESeqAnalysis 0.1.14 (2019-03-29)

Minor changes:

  • Compatibility update for basejump v0.10 release. Some plotting code dependencies have been split out to firestarter and minimalism packages. We have updated the internal code dependencies to reflect these changes. This includes plotCounts, plotDEGHeatmap (i.e. plotHeatmap), and plotDEGPCA (i.e. plotPCA).
  • Updated documentation on global formals, which now use acid prefix instead of basejump.

DESeqAnalysis 0.1.15 (2019-04-03)

New functions:

  • resultsMatrix: Utility function that quickly aggregates DESeqResults values for multiple contrasts into a single matrix. Currently supports return of log2FoldChange, stat, or padj values.

Minor changes:

  • Reorganized unit tests and improved code coverage.

DESeqAnalysis 0.1.16 (2019-04-08)

Major changes:

  • export: Removed humanize argument.
  • plotCounts: Removed transform argument.
  • plotDEGHeatmap, plotDEGPCA: Removed counts argument.
  • plotMA, plotVolcano: Improved color support and gene-to-symbol handling.

Minor changes:

  • topTables: Simplifed internal method code for DESeqAnalysis class.
  • Consistently importing British spelling variants for ggplot2 functions.
  • Updated unit tests for plotting functions.

DESeqAnalysis 0.1.17 (2019-04-08)

Bug fixes to improve handling of DESeqDataSet generated using RefSeq gene annotations.

Minor changes:

  • contrastNames: Improved internal regular expression matching to properly detect a contrast factor prefix that contains an underscore. This now works by checking against the column names of colData internally.
  • topTables: geneID, geneName, and geneBiotype are now optional columns.
  • Updated Travis CI configuration to use rnaseq Docker image.

DESeqAnalysis 0.1.18 (2019-04-23)

Minor changes:

  • NAMESPACE and documentation updates, incorporating new AcidPlots package.

DESeqAnalysis 0.1.19 (2019-04-23)

Minor changes:

  • Converted resultsMatrix to an S4 generic and added initial support for DESeqAnalysis and DESeqAnalysisList class objects.

DESeqAnalysis 0.1.20 (2019-04-25)

New functions:

  • Now exporting lfcShrinkType, and transformType, which were previously used internally but are generally useful.

Major changes:

  • plotDEGHeatmap: Improved default color breaks. Now defaults to blue-black-yellow default color scheme (see AcidPlots::blueYellow).
  • Removed internal .matchResults function in favor of consistently using results instead throughout the package.

Minor changes:

  • Slotting lfcShrink into object is now optional again.
  • Added lfcShrink argument support to plotDEGHeatmap, topTables, and export.
  • plotMA, plotVolcano: Now suppressing duplicate gene message returned by internal Gene2Symbol call, which isn’t informative here.
  • Added lfcThreshold and lfcShrink information on plots, where applicable.

DESeqAnalysis 0.1.21 (2019-04-26)

New functions:

  • plotDEGUpset: Support for easily plotting bidirectional (up/down) DEG intersections across contrasts, using the UpSetR package.

Minor changes:

  • Improved show method to include alpha and lfcThreshold information.
  • topTables: Added lfcShrink support.

DESeqAnalysis 0.1.22 (2019-04-28)

New functions:

  • plotPCA: Added improved method support for DESeqTransform, masking the method exported in DESeq2. Also added corresponding method support for DESeqAnalysis class, which uses DESeqTransform method internally.

Minor changes:

  • Removed plotMA2 export, which keeps DESeq2 plotMA method as an alias.