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Version 0.2

DESeqAnalysis 0.2.0 (2019-07-23)

Version bump, reflecting change in basejump dependency.

DESeqAnalysis 0.2.1 (2019-07-30)

Minor changes:

  • Updated basejump dependencies.
  • Improved code coverage and documentation.
  • Updated example dataset, based on latest acidtest RangedSummarizedExperiment.

DESeqAnalysis 0.2.2 (2019-08-02)

New functions:

  • plotBaseMean: Quickly visualize the count distribution across all samples.

Minor changes:

  • Improved Dockerized Travis CI configuration, using new Rcheck repo.

DESeqAnalysis 0.2.3 (2019-08-06)

Minor changes:

  • Improved documentation consistency by using shared roxygen params from new AcidRoxygen package.
  • Updated basejump dependency versions.

DESeqAnalysis 0.2.4 (2019-08-20)

Minor changes:

  • Removed dplyr dependencies in plotMA and plotVolcano. Reworked internal code using base R methods against DataFrame class instead of tbl_df.
  • Split out documentation on S4 generator functions into separate Rd files.
  • Updated basejump dependecy versions.
  • topTables: Now using DataFrame-oriented internal code to return the kable output, rather than relying upon tbl_df with dplyr.

DESeqAnalysis 0.2.5 (2019-08-27)

Minor changes:

  • Requiring R 3.6. Updated basejump and Bioconductor dependencies.
  • Improved consistency of DataFrame usage inside plotMA and plotVolcano, using our leftJoin method internally.

DESeqAnalysis 0.2.6 (2019-09-09)

New functions:

  • importPairwiseContrasts: Quickly import pairwise contrasts definining numerator and denominator for a specified group.

DESeqAnalysis 0.2.7 (2019-09-11)

Minor changes:

  • Bug fixes for contrast name handling with user-defined resultsNames. DESeqAnalysis methods now stash contrast name into metadata as contrastName for DESeqResults objects, which allows for easier contrast name handling inside plotting and other markdown functions. We needed to add a new useStash argument for contrastName that disables this behavior, so contrastSamples can pull the samples from a pairwise contrast easily.

DESeqAnalysis 0.2.8 (2019-09-17)

New functions:

  • apeglmContrast: New utility function that enables lfcShrink using apeglm without having to mentally deal with coef argument.

Major changes:

  • Now attached DESeq2 automatically via “Depends” in DESCRIPTION.

Minor changes:

  • plotBaseMean: Added argument support to define colors and disable summary statistics lines. Simplified internal passthrough in DESeqAnalysis, DESeqDataSet, and DESeqResults methods.

DESeqAnalysis 0.2.9 (2019-10-09)

New functions:

  • matchMetadataFiles: Quickly generate a mapping data frame of user input metadata sample names to the expected tximport quant directory names (e.g. salmon, kallisto output). This is useful when a user provides metadata that doesn’t match the FASTQ names exactly.
  • prepareTximportFiles: Automatically assigns valid sample names to tximport quant file import. Tested primarily against salmon and kallisto files.

DESeqAnalysis 0.2.10 (2019-10-16)

Minor changes:

  • plotDEGHeatmap, plotDEGPCA: Hardened methods against input with very few DEGs (less than 10). Simplified internal method passthrough to no longer rely upon matchArgsToDoCall function.
  • plotBaseMean: Now exporting numeric method, which is the basis for DESeqDataSet and DESeqResults methods.

DESeqAnalysis 0.2.11 (2019-11-12)

Major changes:

  • Renamed results argument to i for DESeqAnalysis methods, where applicable. This improves consistency with Bioconductor conventions (similar to assay method, which also uses i for position). Note that previous usage of results is now defunct and should intentionally error.

Minor changes:

  • resultsMatrix: Added support for baseMean aggregation, and improved documentation.
  • Updated basejump dependency versions.
  • Added tximport as a suggested package.
  • Updated dependencies to require Bioconductor 3.10 release.
  • Added plotHeatmap, plotCorrelationHeatmap, and plotQuantileHeatmap method support, which extracts DESeqTransform object internally and hands off to SummarizedExperiment methods defined in AcidPlots.

DESeqAnalysis 0.2.12 (2019-11-18)

Minor changes:

  • plotCounts: Added method support for DESeqTransform. Also added a transform argument to DESeqAnalysis method, which allows the user to easily plot variance-stabilized counts using the slotted DESeqTransform object.

DESeqAnalysis 0.2.13 (2019-11-19)

Minor changes:

  • Deprecated apeglmContrast in favor of modified S4 method approach now defined in apeglmResults. The internal code is otherwise unmodified.
  • plotDEGHeatmap: Simplified argument handling and internal passthrough to plotHeatmap SummarizedExperiment method defined in AcidPlots.

DESeqAnalysis 0.2.14 (2019-12-04)

Minor changes:

  • deg: Fixed DESeqAnalysis method passthrough to DESeqResults, allowing use of alpha and lfcThreshold, for post-hoc cutoffs.

DESeqAnalysis 0.2.15 (2019-12-13)

Minor changes:

  • Now allowing the user to override internal alpha and lfcThreshold for these plots: plotDEGHeatmap, plotDEGPCA, plotDEGUpset, plotMA, plotVolcano.

DESeqAnalysis 0.2.16 (2019-12-18)

New functions:

  • resultsDiff: Compare the effect difference between two DESeqResults contrasts. Useful for evaluating the relative effect of compounds, RNAi clones, CRISPR guides, for example.

Minor changes:

  • contrastSamples: Added support for interaction effect (difference of differences) contrasts. For example: “group_B_vs_A_group_C_vs_A_effect”.
  • plotCounts: Added samples argument support for DESeqAnalysis method. This is useful for quick sample selection when generating plots.
  • Improved internal consistency of lfcShrink handling in results calls. Note that reuslts still defaults to lfcShrink = FALSE, whereas other plotting and results table functions default to lfcShrink = TRUE.
  • deg: Added alpha and LFC information in message.

DESeqAnalysis 0.2.17 (2020-01-03)

New functions:

  • combine: Method support for combining multiple results contrasts into a single DESeqAnalysis object. Note that the internal DESeqDataSet and DESeqTransform objects defined in x and y must match.

DESeqAnalysis 0.2.18 (2020-01-20)

Minor changes:

  • Updated basejump dependencies. Namely, bioverbs package has been renamed to AcidGenerics, prior to CRAN submission.

DESeqAnalysis 0.2.19 (2020-03-16)

Minor changes:

  • Resaved example test data set, using Ensembl 99 annotations.
  • Updated documentation using roxygen2 v7.1.

DESeqAnalysis 0.2.20 (2020-05-12)

Minor changes:

  • Split out setValidity call separately from setClass.
  • updateObject: FGSEAList method now uses ... and verbose arguments, as defined in the S4 generic.

DESeqAnalysis 0.2.21 (2020-07-29)

Major changes:

  • Added support for baseMeanThreshold, where applicable. Applies primarily to deg, plotDEGHeatmap, plotDEGPCA, plotMA, and plotVolcano, and resultsTables.
  • Reworked internal code that handles DEG extraction. Note that lfcThreshold and baseMeanThreshold now use >= logic rather than previous > approach. The alpha cutoff still uses > operator logic.

Minor changes:

  • Removed UpSetR dependency, in preparation for future switch to ggupset.