NEWS.md

In acidgenomics/DESeqAnalysis: Acid Genomics DESeq2 Analysis Utilities

Release notes

DESeqAnalysis 0.7.1 (2024-03-27)

Minor changes:

• Updated dependencies to Bioconductor 3.18.
• Ensured that validObject calls are enclosed within assert.
• Relaxed validObject assert checks on legacy DESeqResults methods.
• Resaved minimal example objects for unit tests.
• Improved lfcShrinkType for legacy DESeqResults objects.

DESeqAnalysis 0.7.0 (2023-10-04)

Minor changes:

• Removed dependency on stringi package, in favor of strMatch from AcidBase.
• export: Reworked methods to use AcidGenerics convention instead of BiocIO.
• Now enforcing strict camel case for all function names.
• Renamed plotDEGHeatmap to plotDegHeatmap.
• Renamed plotDEGPCA to plotDegPca.
• Renamed plotDEGStackedBar to plotDegStackedBar.
• Renamed plotDEGUpset to plotDegUpset.
• Renamed plotLFC to plotLfc.
• Renamed plotMA to plotMa. Now using AcidGenerics instead of BiocGenerics.
• Renamed plotPCA to plotPca. Now using AcidGenerics instead of BiocGenerics.

DESeqAnalysis 0.6.12 (2023-08-15)

Minor changes:

• Reworked internal ggplot2 code to use data pronouns (.data) instead of rlang syntactic sugar (!!/sym).
• Using updated AcidPlots functions: acid_scale_color_discrete instead of autoDiscreteColorScale and acid_discrete_coord_flip instead of acid_coord_flip.

DESeqAnalysis 0.6.11 (2023-07-25)

Minor changes:

• sanitizeTximportIdentifiers: Fixed typo in identifier check pattern.

DESeqAnalysis 0.6.10 (2023-07-25)

New functions:

• sanitizeTximportIdentifiers: New utility function for sanitizing malformed transcript identifiers returned when importing salmon data generated against GENCODE-aligned BAM files. We hit this edge case when processing Nanopore samples using guppy to minimap2 to BAM with samtools. This edge case has also be observed when importing kallisto data aligned against GENCODE, which also doesn't currently handle transcript identifier sanitization correctly.

DESeqAnalysis 0.6.9 (2023-07-13)

Major changes:

• Updated dependencies to R 4.3 / Bioconductor 3.17.

Minor changes:

• Removed internal calls to basejump package, which has been changed to a meta-package of Acid Genomics packages, without any exports in NAMESPACE. This has been corrected inside of prepareTximportFiles to correctly reference the methods exported in syntactic package.

DESeqAnalysis 0.6.8 (2023-04-28)

Major changes:

• Reworked prepareTximportFiles to work on a directory instead of files.

Minor changes:

• Now classing on DFrame instead of DataFrame virtual class consitently.
• Resaved example deseq and deseqMinimal objects.
• Removed unused matchMetadataToFiles function.

DESeqAnalysis 0.6.7 (2023-02-09)

Minor changes:

• Updated dependencies to Bioconductor 3.16.
• Migrated requireNamespaces import from AcidBase to goalie.

DESeqAnalysis 0.6.6 (2022-10-25)

Major changes:

• export: Reduced the number of exported methods, to match the new conventions defined by pipette. Note that con is now required instead of dir for the target directory.

Minor changes:

• Tightened up dependency requirements.
• Improved consistency of internal goalie boolean functions.

DESeqAnalysis 0.6.5 (2022-08-30)

Minor changes:

• Updated package to roxygen2 7.2.1.
• results: Now defaults to quiet = TRUE by default, to reduce the amount of message spam in bcbioRNASeq R Markdown templates.

DESeqAnalysis 0.6.4 (2022-06-09)

Minor changes:

• Improved Windows CI compatibility, using tempdir2 and unlink2.

DESeqAnalysis 0.6.3 (2022-05-25)

Minor changes:

• Removed deprecated plotMeanAverage and apeglmContrast functions from NAMESPACE, to avoid collisions with updates in bcbioRNASeq package.

DESeqAnalysis 0.6.2 (2022-05-24)

Major changes:

• Reworked and simplified topTables as markdownTables.
• Simplified resultsTables return to always return as DataFrameList containing subset DESeqResults. Previously tbl_df option was available, but this has been removed in favor of Bioconductor S4Vectors support instead.
• Improved code coverage of export, markdownTables, and resultsTables, to ensure that we never drop rownames.

DESeqAnalysis 0.6.1 (2022-05-18)

Minor changes:

• Hardened resultsTables and topTables to work with minimal DESeqDataSet that doesn't contain gene names and additional metadata in rowData.
• Improved plotDEGStackedBar and plotDEGUpset to early return with alert warning for objects without DEGs.
• Resaved example objects and added new deseqMinimal object, that contains an unusually small DESeqDataSet without metadata, which is useful for testing edge case handling in our plotting functions.
• Updated lintr checks and migrated to testthat 3e for unit tests.
• Now consistently using Map instead of mapply, as recommended by lintr.
• plotBaseMean now longer exporting integer method -- using internally only.

DESeqAnalysis 0.6.0 (2022-05-06)

Major changes:

• Package now requires R 4.2 / Bioconductor 3.15.

Minor changes:

• Reworked internal droplevels calls against SummarizedExperiment using new droplevels2 approach, which provides better compatibility with Bioconductor 3.15 release.
• Reworked internal handoff to ggplot, using as.data.frame coercion instead of as_tibble.

DESeqAnalysis 0.5.0 (2022-04-15)

New functions:

• plotContrastScatter: Visualize expression between numerator and denominator for a contrast of interest.
• plotLFC: Plot log2 fold change distributions for all contrasts in the DESeq2 analysis.

Major changes:

• Updated dependencies to R 4.1 / Bioconductor 3.14.
• export: Updated method to inherit BiocIO conventions now used in basejump, which now rely on con argument.
• Added as.DESeqDataSet and as.DESeqTransform coercion methods.

Minor changes:

• plotPCA: Tightned up method export to only work on DESeqAnalysis object, so we don't conflict with DESeqTransform method defined in DESeq2.
• plotVolcano: Hardened against edge case where visualization of a specific gene is requested, but contains a censored adjusted P value.
• Updated example deseq object.
• Added basejump as a library load in DE template.
• contrastSamples: Improved documentation.
• Package code is now formatted according to styler conventions.

DESeqAnalysis 0.4.4 (2021-08-02)

Minor changes:

• apeglmResults: Relaxed assert check on P values when applying adaptive shrinkage via apeglm model.

DESeqAnalysis 0.4.3 (2021-07-27)

Minor changes:

• plotVolcano: Bug fix for plot labels not mapping correctly. Expecting "lfcCol", "negLogAlphaCol" internally, but these were incorrectly mapped to the values expected for plotMA instead. Thanks to @kokyriakidis for noticing this.

DESeqAnalysis 0.4.2 (2021-07-20)

Minor changes:

• Improved R Markdown template for differential expression report, and added code coverage for rmarkdown::render call in unit tests.

DESeqAnalysis 0.4.1 (2021-06-29)

Minor changes:

• Needed to update internal calls to guide function defined in ggplot2, which has deprecated use of logical FALSE in favor of "none".

DESeqAnalysis 0.4.0 (2021-03-15)

New classes:

• DESeqResultsList: New class and corresponding generator function that enables quick looping operations across related DESeqResults objects. This can be useful instead of DESeqAnalysisList approach for cases where we don't have all of the original DESeqDataSet objects used to generate the corresponding DESeqResults, which can happen with commercial sequencing vendors and analysis platforms.

Major changes:

• Reworked and improved manual limit handling for plotMA and plotVolcano. By default, this behavior is unchanged from previous release, but now limit overrides can be defined similar to the approach in DESeq2 that uses geneplotter engine internally.

Minor changes:

• Improved information in subtitles for MA, volcano, and other DEG plots.
• alphaThreshold and lfcThreshold return sensible defaults for minimal DESeqResults objects created by coercion of a DataFrame directly.

DESeqAnalysis 0.3.12 (2021-02-17)

Minor changes:

• DESeqAnalysis: Relaxed check for gene identifiers in mcols of rowRanges of nested DESeqDataSet inside data slot. Resolves issue #61.
• Updated internal dependencies. Now requiring basejump v0.14.8+, which also depends on at least Bioconductor 3.12.

DESeqAnalysis 0.3.11 (2021-02-10)

Minor changes:

• NAMESPACE updates, simplifying the number of imported packages following the basejump v0.14 release.

DESeqAnalysis 0.3.10 (2020-10-28)

Major changes:

• Added subsetting extract method support via [ for DESeqAnalysis class. Code works internally similar to method defined for bcbioRNASeq.
• Added method support for some important base methods: rownames, colnames, names, and dimnames for DESeqAnalysis class.

Minor changes:

• degIntersection: Added return = "names" option, which is useful for generating intersection subset tables.

DESeqAnalysis 0.3.9 (2020-10-08)

Minor changes:

• Updated package dependency version requirements.

DESeqAnalysis 0.3.8 (2020-09-21)

Minor changes:

• Migrated extra mode internal code from resultsTables directly into results, so we can hand-off to new methods defined in acidgsea package that depend on DESeqResults object (i.e. geneSetResults). The resultsTables function still behaves the same as previous releases.
• plotDEGStackedBar: Added support for orderBySize argument.
• degPerContrast: Removed unnecessary n argument; use return instead.

DESeqAnalysis 0.3.7 (2020-09-18)

Minor changes:

• results: Bug fix for logical check on lfcShrink return. The internal use of identical here is too strict, as lfcShrink can return cause attribute from goalie.
• lfcShrink: Hardened logical return, ensure goalie cause attribute removal.

DESeqAnalysis 0.3.6 (2020-08-25)

Minor changes:

• plotDEGPCA: Updated internal title and subtitle handoff to plotPCA.
• Quieted down messages in plotDEG* functions. This information is shown in the plots and doesn't need to be messaged.

DESeqAnalysis 0.3.5 (2020-08-18)

Minor changes:

• degIntersection: Bug fix for column names not returning as expected.

DESeqAnalysis 0.3.4 (2020-08-18)

New functions:

• degIntersection: Utility function that will return the number of times a DEG is detected across contrasts.

DESeqAnalysis 0.3.3 (2020-08-17)

Minor changes:

• apeglmResults: Simplified default arguments and disabled ... passthrough to lfcShrink, which is a bit confusing. Note that DESeq and lfcShrink are now called internally with parallel = TRUE.

DESeqAnalysis 0.3.2 (2020-08-13)

Minor changes:

• Added i argument support to degPerContrast, and the plotting functions plotDEGUpset and plotStackedBar, which call degPerContrast internally. This allows the user to pick specific contrasts of interest to plot.
• plotDEGStackedBar: Now allowing the user to pick only up- or down-regulated genes, which can be useful.
• Bug fix for apeglmResults cli display code.

DESeqAnalysis 0.3.1 (2020-08-07)

Minor changes:

• Adjusted minimum dependency versions so package will build on bioconda.

DESeqAnalysis 0.3.0 (2020-08-05)

Major changes:

• DESeqAnalysis object now supports stashing of threshold metadata:
• alphaThreshold.
• lfcShrink: whether to use (adaptie) shrunken LFC values or not.
• lfcThreshold (for post-hoc cutoffs).
• baseMeanThreshold. These are defined in the metadata slot of the object and can be accessed/ modified with corresponding S4 generics.
• Updated default differential expression R Markdown template to support additional parameters:
• alpha_threshold
• base_mean_threshold
• contrast_samples
• lfc_shrink
• lfc_threshold

Minor changes:

• Switched to cli package for more informative messages.

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.

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 0.2.19 (2020-03-16)

Minor changes:

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

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 0.2.17 (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 0.2.16 (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 0.2.15 (2019-12-13)

Minor changes:

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

DESeqAnalysis 0.2.14 (2019-12-04)

Minor changes:

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

DESeqAnalysis 0.2.13 (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 0.2.12 (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 0.2.11 (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 0.2.10 (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 0.2.9 (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 0.2.8 (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 0.2.7 (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 0.2.6 (2019-09-09)

New functions:

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

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 0.2.4 (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 0.2.3 (2019-08-06)

Minor changes:

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

DESeqAnalysis 0.2.2 (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 0.2.1 (2019-07-30)

Minor changes:

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

DESeqAnalysis 0.2.0 (2019-07-23)

Version bump, reflecting change in basejump dependency.

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.

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 0.1.20 (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 0.1.19 (2019-04-23)

Minor changes:

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

DESeqAnalysis 0.1.18 (2019-04-23)

Minor changes:

• NAMESPACE and documentation updates, incorporating new AcidPlots package.

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 0.1.16 (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 0.1.15 (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 0.1.14 (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 0.1.13 (2019-03-23)

Minor changes:

• Migrated code to Acid Genomics.

DESeqAnalysis 0.1.12 (2019-03-18)

Minor changes:

• Updated differential expression template and dependencies.

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 0.1.10 (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 0.1.9 (2019-02-12)

Minor changes:

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

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 0.1.7 (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 0.1.6 (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 0.1.5 (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 0.1.4 (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 0.1.3 (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 0.1.2 (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 0.1.1 (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 0.1.0 (2018-11-19)

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

acidgenomics/DESeqAnalysis documentation built on March 27, 2024, 10:32 p.m.