NEWS.md

In acidgenomics/pfgsea: Acid Genomics GSEA

Release notes

AcidGSEA 0.9.0 (2023-10-04)

Major changes:

• Now enforcing strict camel case for all function names.
• Renamed primary FGSEAList class to FgseaList.
• Removed BiocParallel in favor of parallel.
• Reworked export method to conform to new changes in pipette package. Namely, we have reworked the generic to be simpler than BiocIO variant.

AcidGSEA 0.8.9 (2023-08-15)

Minor changes:

• Now requiring R 4.3 / Bioconductor 3.17.
• Reworked internal ggplot2 code to use data pronouns instead of rlang syntactic sugar.
• Updated NAMESPACE related to AcidPlots.

AcidGSEA 0.8.8 (2023-04-28)

Major changes:

• Reworked handling of NCBI (Entrez) gene identifiers.
• Now classing on DFrame instead of DataFrame virtual class, where applicable.
• Also classing on GRanges directly instead of GenomicRanges virtual class, where applicable.

AcidGSEA 0.8.7 (2023-02-09)

Minor changes:

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

AcidGSEA 0.8.6 (2022-10-25)

Major changes:

• Hardened package dependency requirements.
• export: Restricting methods, following conventions now defined in pipette 0.10.0 update.
• Using hasDuplicates internally from goalie.

AcidGSEA 0.8.5 (2022-08-31)

Major changes:

• RankedList Relaxed the internal thresholds for acceptable gene identifier mapping thresholds. Previous cutoffs were a bit too strict and could result in errors with acceptable datasets.
• export: Simplified S4 method to class with con and format arguments defined as required character and missingOrNULL, respectively. Improved the documentation to denote that user should specify a directory as con, and either "csv" or "tsv" as the desired output format.

Minor changes:

• Updated roxygen2 documentation.
• Resolved any Markdown lints using markdownlint.

AcidGSEA 0.8.4 (2022-08-17)

Major changes:

• FGSEAList: Simplified input to use recommended defaults for fgsea passthrough. Note that fgsea now uses fgseaMultilevel by default in Bioconductor 3.15. Object class checks have been updated to reflect this breaking change.

Minor changes:

• RankedList: Fix for ensemblId handling as input.
• Resaved example fgsea object.

AcidGSEA 0.8.3 (2022-06-09)

Minor changes:

• Improved support for Windows CI checks, using tempdir2 and unlink2.

AcidGSEA 0.8.2 (2022-05-26)

Major changes:

• RankedList: Improved keyType support, adding back "geneId", and "ensemblId". Simplified internal code for unlisting nested Entrez identifier keys and ensuring they map 1:1 by oldest identifier.
• RankedList: Function now looks inside geneId and checks against provider metadata defined in rowRanges, in the event that ensemblId or ensemblId mcols are not defined, but the key is in Ensembl or Entrez format.
• RankedList: In the event the user requests keyType of "geneId" or "ensemblId", we now also call stripGeneVersions to sanitize the gene identifiers to remove gene versions.

AcidGSEA 0.8.1 (2022-05-24)

Major changes:

• Reworked topTables as markdownTables, following updated conventions used in other Acid Genomics packages, such as AcidMarkdown and DESeqAnalysis.

Minor changes:

• Updated lintr checks and testthat unit tests.

AcidGSEA 0.8.0 (2022-05-06)

Major changes:

• Package now requires R 4.2 / Bioconductor 3.15.
• Compatibility fixes for breaking changes in pipette package.

AcidGSEA 0.7.0 (2022-04-27)

Major changes:

• Split out basejump dependencies into individual packages.
• Added support for multiple contrasts: plotNES, plotGeneSet, results.
• export method now confirms to BiocIO approach, using con argument.
• RankedList: Tightned up Ensembl reference genome filtering, checking for gene identifiers from primary chromosomes, to avoid unwanted averaging of values from haplotype scaffold gene identifiers. Also added support for proteinCodingOnly, to enable analysis of protein coding genes only, which is disabled by default.
• Reworked our internal Gene2Symbol handling for plot functions.

Minor changes:

• FGSEAList and RankedList: Reworked default formals for keyType and value.
• Added basejump as a dependency to R Markdown template.
• Relaxed gene-to-symbol class checks for RankedList S4 class.
• Improved rich text formatting for CLI messages, where applicable.
• Added an additional assert check for gene identifier overlap prior to internal fgsea handoff.
• plotLFC: Improved labeling of axes.
• prepareGeneSetFiles: Reworked file name detection for MSigDb.
• Improved internal code for returning results for all contrasts.

AcidGSEA 0.6.4 (2021-07-21)

Minor changes:

• RankedList: Improved handling of duplicate Entrez gene identifiers, such as is the case in the bcbioRNASeq F1000 example dataset.
• Reorganized and consolidated S4 method exports.

AcidGSEA 0.6.3 (2021-06-29)

Minor changes:

• RankedList: Improved column name sanitization and handling for input DESeqResults object, avoiding conflicts with Gene2Symbol object.
• Improved unit tests to no longer rely on gene sets saved in ~/msigdb.

AcidGSEA 0.6.2 (2021-03-16)

Minor changes:

• Updated basejump dependencies.
• Resaved example fgsea object (FGSEAList).
• Updated unit tests.

AcidGSEA 0.6.1 (2021-03-04)

New functions:

• prepareGeneSetFiles: MSigDb utility function for easy matching of default GMT gene files to use for GSEA. Matches the symbol files by default.

Major changes:

• RankedList and FGSEAList method support has been improved for minimal DESeqResults and DataFrame objects. These approaches are intended primarily for analysis of files from collaborators where we don't necessarily have the complete set of DESeq2 analysis files, and therefore cannot construct a DESeqAnalysis object.

Minor changes:

• RankedList now supports keyType, which defaults to gene name (a.k.a. symbol), but now also supports original gene identifier. This alternative option is useful when working with the clusterProfiler package and is used in the bcbioRNASeq template.

AcidGSEA 0.6.0 (2021-02-17)

Major changes:

• Reworked and simplified NAMESPACE and package dependencies, following basejump v0.14 release series update.
• Removed BiocParallel as a required import.

AcidGSEA 0.5.0 (2020-10-10)

Major changes:

• Renamed package to AcidGSEA from acidgsea.

Minor changes:

• Migrated generics to AcidGenerics: geneSetNames, plotLFC, plotNES.

acidgsea 0.4.0 (2020-09-26)

Major changes:

• FGSEAList: Reworked primary method to use DESeqAnalysis instead of RankedList as input. The RankedList object is now calculated automatically internally.
• Now slotting gene sets inside the FGSEAList object.
• gmtFiles argument has been renamed to geneSetFiles.

New functions:

• geneSetResults: Extract gene set expression values (from DESeqResults).
• leadingEdge: New accessor that returns leading edge genes from GSEA run.
• results: Extract GSEA results from object (from fgsea return).

acidgsea 0.3.2 (2020-08-05)

Major changes:

• Simplified internal handling of alpha (now consistently referfed to as "alphaThreshold") and nesThreshold.
• Added alphaThreshold and nesThreshold S4 generic support.
• These name chanages better match the syntax used in DESeqAnalysis v0.3.

acidgsea 0.3.1 (2020-07-24)

New functions:

• plotGeneSet: Split out internal gene set plotting code used previously in plotEnrichedGeneSets. This is a modified variant of fgsea::plotEnrichment that allows for additional color customization.

Major changes:

• Updated minimum R dependency to 4.0.
• plotEnrichedGeneSets: Now calls new plotGeneSet function internally.

Minor changes:

• Removed UpSetR dependency, based on update to AcidPlots package.
• Removed plotCounts method, in favor of plotHeatmap usage.

acidgsea 0.3.0 (2020-05-24)

Major changes:

• FGSEAList: Converted function to an S4 generic. Previously the main arguemnt was named rankedList, but this has been renamed to object. A RankedList object can still be passed in as the first object in the function call. This change was necessary for adding GSEA support in pointillism single-cell RNA-seq analysis toolkit.

Minor changes:

• RankedList: Added support for DataFrame class, which is used inside pointillism package update.
• RankedList: Added gene2symbol argument support for matrix model. Using this for cluster matrix in pointillism for scRNA-seq using output from edgeR (or DESeq2) for per-cluster marker analysis.

acidgsea 0.2.1 (2020-05-12)

Minor changes:

• Split out setValidity from setClass for S4 class definitions.
• updateObject: Added support for ... and verbose arguments defined in the S4 generic.

acidgsea 0.2.0 (2020-03-18)

Major changes:

• Renamed package from "pfgsea" to "acidgsea". Additional GSEA methods including the Broad GSEA Preranked algorithm and support for Jean Fan's liger package are planned for a future update, so it no longer makes sense to pin the package name specifically to fgsea.
• Reworked internally enriched gene set filtering and handoff. Affected functions: enrichedGeneSets, plotEnrichedGeneSets, and plotEnrichedUpset.

Minor changes:

• convertToHuman: Updated working example to use Ensembl 99 release, as archived releases are currently unavailable via biomaRt until March 24, due to Ensembl server migration. See Ensembl website for details.
• Updated minimal example gsea object.
• Updated unit tests and working examples to reflect package name change.

pfgsea 0.1.17 (2020-01-27)

Minor changes:

• Now using cli package for interactive messages.

pfgsea 0.1.16 (2020-01-20)

Minor changes:

• NAMESPACE update required for changes in basejump v0.12.

pfgsea 0.1.15 (2019-11-20)

New functions:

• plotCounts, plotHeatmap: Added initial FGSEAList method support.

Major changes:

• plotGSEATable: Made defunct, since this visualization doesn't render very reliably in R Markdown output. Consider using a heatmap approach instead.

pfgsea 0.1.14 (2019-10-11)

Minor changes:

• export: Updated internal code to handle leadingEdge as list class.
• Updated R Markdown template to use "object" as primary param.

pfgsea 0.1.13 (2019-08-28)

Major changes:

• Reworked internal code to no longer depend on dplyr.
• Improved internal handling using DataFrame rather than data.table.

pfgsea 0.1.12 (2019-07-30)

Minor changes:

• Updated basejump dependency versions.
• Updated working examples and improved documentation.

pfgsea 0.1.11 (2019-07-24)

pfgsea 0.1.10 (2019-07-17)

Minor changes:

• Updated basejump dependency.
• Improved Travis CI docker configuration.

pfgsea 0.1.9 (2019-06-26)

New functions:

• convertToHuman: Utility that maps orthologs onto human genes, so we can perform GSEA. Added map argument support, to speed up multiple calls.

pfgsea 0.1.8 (2019-06-12)

New functions:

• Initial method support for convertToHuman, which allows for easy ortholog conversion to HUGO (HGNC) identifiers.

Minor changes:

• Improved render.R script for looping multiple DESeqAnalysis objects.
• Improved dockerized Travis CI checks.
• Improved code coverage checks for export method.

pfgsea 0.1.7 (2019-04-30)

Major changes:

• Reworked language to use "collection" consistently instead of mixing/matching "geneSet" and "pathway", which isn't appropriate. Relevant function arguments have been updated to reflect this change.
• Now exporting collectionNames instead of pathwayNames.
• enriched and plotEnrichedUpset have been updated to return per collection (e.g. hallmark gene set), which makes more sense. We don't want to visualize overlap across collections, since these are often completely different classes (e.g. c1-c7 will never have overlap).

pfgsea 0.1.6 (2019-04-29)

New functions:

• pathwayNames, contrastNames: Accessor functions for pathway (e.g. MSigDb) and differential expression contrast names.
• enriched method support for FGSEAList class. Useful for returning a list directionally significant pathways, per contrast. Primarily intended for use at the moment with plotEnrichedUpset.
• plotEnrichedUpset: Utility function that makes it easy to compare enrichment groups across contrasts, via an UpSet plot.

Major changes:

• Added combine method support for FGSEAList, allowing us to easily combine GSEA results from multiple datasets. Primarily intended for downstream visualization using an UpSet plot (see plotEnrichedUpset).

Minor changes:

• Improved show method support for FGSEAList, showing pathwayNames and contrastNames more clearly.

pfgsea 0.1.5 (2019-04-25)

Minor changes:

• S4 generic reexport documentation fixes.

pfgsea 0.1.4 (2019-04-23)

Minor changes:

• Switch to importing graphics code from AcidPlots package instead of now defunct minimalism package. Default ggplot2 theme has been renamed from theme_paperwhite to acid_theme_light.

pfgsea 0.1.3 (2019-04-17)

Minor changes:

• Updated Travis CI configuration to use rnaseq Docker image.
• Miscellaneous documentation improvements.

pfgsea 0.1.2 (2019-04-10)

Major changes:

• Deleted list to FGSEAList coercion method.

Minor changes:

• pfgsea: Renamed bpparam argument to BPPARAM, to match Bioconductor. Also now reexporting BiocParallel::bpparam.
• Added gsea minimal working example dataset, for unit testing.
• Added documentation working examples, using gsea data.
• Updated NAMESPACE for theme_paperwhite. Now reexporting this function.

pfgsea 0.1.1 (2019-04-01)

Minor changes:

• NAMESPACE updates to reflect changes in basejump package.
• Now importing theme_paperwhite from minimalism package.

pfgsea 0.1.0 (2019-03-23)

• Initial stable release.
• Moved code to Acid Genomics.

pfgsea 0.0.7 (2019-03-18)

Minor changes:

• Updated basejump and DESeqAnalysis dependencies.

pfgsea 0.0.6 (2019-03-11)

Minor changes:

• Improved parameterized object passthrough in R Markdown template.
• Added Travis CI and AppVeyor CI coverage.

pfgsea 0.0.5 (2019-02-04)

Major changes:

• Now exporting FGSEAList and RankedList S4 classes.
• Reworked plotEnrichment(), plotGSEATable(), and topTables() to use FGSEAList object.
• Renamed statsList() to RankedList(), and switched to S4 method approach.
• Updated R Markdown template to reflect these function reworkings.

pfgsea 0.0.4 (2019-01-15)

Minor changes:

• Documentation fixes and other code cleanup to pass lintr checks.

pfgsea 0.0.3 (2018-12-17)

New functions:

• statsList: Return preranked GSEA stats list.

Major changes:

• Added FGSEA R Markdown template.

pfgsea 0.0.2 (2018-12-14)

Major changes:

• Switched to using goalie for assert checks instead of assertive.

Minor changes:

• Added README.
• Set up lintr checks.
• Set up pkgdown website.
• Miscellaneous documentation improvements.

pfgsea 0.0.1 (2018-11-26)

Initial release.

acidgenomics/pfgsea documentation built on Oct. 18, 2023, 11:12 a.m.