NEWS.md

In acidgenomics/r-acidexperiment: Acid Genomics Summarized Experiment

Release notes

AcidExperiment 0.5.4 (2023-12-01)

Minor changes:

• EnsemblToEntrez: Updated unit test to reflect breaking change in pending AcidGenomes package update.

AcidExperiment 0.5.3 (2023-10-27)

Minor changes:

• melt: Needed to ensure that join column is factor, to avoid unwanted type switch during leftJoin step.

AcidExperiment 0.5.2 (2023-10-05)

Minor changes:

• Removed export method for MultiAssayExperiment, which has migrated to cBioPortalAnalysis package instead. The MultiAssayExperiment package introduces too many unwanted dependencies.

AcidExperiment 0.5.1 (2023-10-05)

Minor changes:

• convertSampleIdsToNames: Quiet down this function when no sample name conversion is necessary.

AcidExperiment 0.5.0 (2023-10-04)

Major changes:

• Starting a new release series, based on breaking changes in other Acid Genomics dependency packages.
• Now enforcing strict camel case for all function names.
• Replaced usage of "2" with "To" in relevant generics.
• export: Updated method to use AcidGenerics conventions rather than BiocIO.
• Replaced usage of stringi with AcidBase variants.

Minor changes:

• AcidExperimentTestsUrl: No longer uses specific version.

AcidExperiment 0.4.6 (2023-04-27)

Minor changes:

• Now consistently using DFrame instead of DataFrame; GRanges instead of GenomicRanges in S4 coercion and method definitions.
• Updated package to use new Ensembl2Ncbi and Ncbi2Ensembl generics now defined in AcidGenomes, instead of previous Ensembl2Entrez and Entrez2Ensembl. We are now using "NCBI" consistently across packages instead of the legacy "Entrez" name.

AcidExperiment 0.4.5 (2023-02-09)

Minor changes:

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

AcidExperiment 0.4.4 (2022-10-25)

Major changes:

• export: Added initial method support for MultiAssayExperiment.

Minor changes:

• export: Hardened method to only use con, dropping support for legacy dir approach. These methods have been restricted based on the pending pipette v0.10 release series.
• Hardened dependencies to match Bioconductor 3.15 release series more clearly.

AcidExperiment 0.4.3 (2022-06-02)

Minor changes:

• Hardened tempdir and unlink calls in unit tests and working examples, to improve compatibility in Windows testing environment.

AcidExperiment 0.4.2 (2022-05-25)

Minor changes:

• export: Hardened SummarizedExperiment against edge cases where no assays, colData, or rowData are defined.

AcidExperiment 0.4.1 (2022-05-23)

Minor changes:

• Updated lintr checks and testthat unit tests.

AcidExperiment 0.4.0 (2022-05-04)

Major changes:

• Now requiring R 4.2 / Bioconductor 3.15.
• Lightened package by eliminating strong dependencies on scales, sessioninfo, and stringr package. Also removed dependency on tibble package via pipette.
• makeSummarizedExperiment will conditionally slot session_info from sessioninfo package if installed, otherwise will fall back to sessionInfo from utils package.

Minor changes:

• Reworking factor level support as droplevels2 instead of droplevels, to avoid method collisions with Bioconductor 3.15.
• Reformatted package code using styler conventions.

AcidExperiment 0.3.0 (2022-03-11)

Major changes:

• export: Reworked SummarizedExperiment to use new BiocIO generic approach. This generic now uses con instead of dir to define the directory path. Note that previously, the object name would be defined as a subdirectory when using dir to define the path. We are currently keeping this legacy approach when using dir, but no attempt to parse the object name and create a corresponding subdirectory is employed when using the new con argument.
• convertGenesToSymbols and convertSymbolsToGenes: Simplified the number of exported methods to now simply dispatch on SummarizedExperiment. Added support for new strict mode check, which intentionally does not allow propagation of any NA values during interconversion steps.

Minor changes:

• selectSamples: The function now automatically relevels factors defined in colData.
• Reworked internal code to no longer depend on formalsList and getNameInParent from AcidBase package. Note that getNameInParent is now only exported in goalie package. Also removed import of now defunct as.data.frame methods previously defined in pipette package.
• S4 methods are now defined alphabetically in package documentation.
• Hardened internal mapGenes code to no longer use tryCatch call and silently error on map failure.
• selectSamples: Factors defined in colData are now automatically releveled via internal droplevels call for SummarizedExperiment method.

AcidExperiment 0.2.2 (2021-09-13)

Major changes:

• aggregate: Added support via MARGIN argument to work either row-wise (1; default) or column-wise (2). SummarizedExperiment method has been updated to support these conventions. Corresponding aggregateCols and aggregateRows functions have been simplified to merely wrap an aggregate call with MARGIN argument predefined.
• convertTranscriptsToGenes: Now all assays are aggregated, rather than simplify returning primary counts assay.

Minor changes:

• calculateMetrics: Updated to support assay argument.
• convertGenesToSymbols: Removed unnecessary strict argument for SummarizedExperiment method, and simplified handling of mismatched Gene2Symbol internally.
• estimateSizeFactors now supports assay argument.
• integerCounts now supports assay argument.
• aggregate keeps track of mapping factor used internally for SummarizedExperiment method. This is defined as aggregateRows or aggregateCols in the object metadata.

AcidExperiment 0.2.1 (2021-09-08)

Minor changes:

• Now importing bapply from goalie instead of AcidBase.
• Updated internal gene mapping code to better handle mismatched Gene2Symbol input, which can happen in pointillism package.

AcidExperiment 0.2.0 (2021-09-03)

Major changes:

• Reworked and improved unit tests to achieve 100% code coverage.
• calculateMetrics: Simplifed internal assert checks. The matrix and Matrix methods (handed off from SummarizedExperiment method) now work primarily on rowData instead of rowRanges, since we're not using any genomic coordinates here in checks. Prefiltering (disabled by default, but can be enabled with prefilter = TRUE) now removes column elements (e.g. cells and/or samples) with all mito counts (mitoRatio >= 1) and an artifically high log10FeaturesPerCount >= 1 value. These settings help make 100% code coverage possible on minimal test datasets.
• makeSummarizedExperiment: Improved and fixed CLI messages on detected of mismatched features to be slotted into rowRanges. This can happen when incorrect values are defined in ensemblRelease or gffFile. This should help resolve the cryptic CLI error message seen in bcbioRNASeq issue #170.

Minor changes:

• Made unused matchesGene2Symbol and matchesInterestingGroups functions defunct. These are still reexported in basejump and DESeqAnalysis, which will be cleaned up in future releases.
• Improved and hardened CLI messages. Now using abort instead of stop internally, to support better stylized error messages.
• Now calling toStringInline instead of base toString internally to properly handle string handoff to cli package.
• autopadZeros: SummarizedExperiment method now has sampleNames argument, which allows the user to selectively pad the sample names column sampleNames defined in colData. Enabled by default, matching previous internal behavior.
• estimateSizeFactors: Simplified internal assert checks that look for any zero libSizes. Also improved code coverage to check for specific values returned by type argument.

AcidExperiment 0.1.14 (2021-08-11)

Major changes:

• convertGenesToSymbols: Added strict and quiet arguments. Improved and hardened internal code, improving the verbosity of calls to Gene2Symbol generator. Added additional asserts to ensure that mismatches (e.g. row flipping) don't occur.
• Ensembl2Entrez, Gene2Symbol: Updated formals to passthrough to other primary methods defined in AcidGenomes package.

Minor changes:

• Hardened and expanded code coverage for expected gene-to-symbol mapping behavior in main Gene2Symbol generator, focusing on the format argument.

AcidExperiment 0.1.13 (2021-08-09)

Minor changes:

• Updated package dependency version cutoffs.
• Gene2Symbol: Tightened up internal match.arg handling for format argument, in defined SummarizedExperiment method.

AcidExperiment 0.1.12 (2021-06-10)

Minor changes:

• mapGenesToRownames, mapGenesToIDs, mapGenesToSymbols: Improved the flexibility of gene identifier matching for SummarizedExperiment method. Now also attempts to match against geneSynonyms when defined in rowData, which is incredibly useful for easy matching of deprecated gene names.
• Removed unnecessary Gene2Symbol methods for mapGenesToRownames, mapGenesToIDs, and mapGenesToSymbols.
• matchesGene2Symbol no longer attempts to use the now removed Gene2Symbol method for mapGenesToRownames internally. We simplified this check using the internal .mapGenes function to locate index position instead.

AcidExperiment 0.1.11 (2021-06-04)

Minor changes:

• Updated the documentation to provide compatibility with R 4.1 and Bioconductor 3.13 release.
• Updated dependency versions.

AcidExperiment 0.1.10 (2021-03-10)

Minor changes:

• makeSummarizedExperiment: Relaxed the validity check on syntactically valid names in rownames and colnames of the object. Now the function informs the user with a CLI message instead of erroring.

AcidExperiment 0.1.9 (2021-02-25)

Minor changes:

• Renamed all internal instances of "blacklist" to "denylist".
• Added denylist override option to makeSummarizedExperiment (recommended to be left enabled by default), which will be used in cBioPortalAnalysis package update.

AcidExperiment 0.1.8 (2021-02-22)

Minor changes:

• Now enforcing lower camel case for sampleData return.
• Simplified generic handling for Matrix methods.

AcidExperiment 0.1.7 (2021-02-13)

Minor changes:

• More internal NAMESPACE reworks. IRanges classes now defined in AcidGenerics.

AcidExperiment 0.1.6 (2021-02-11)

Minor changes:

• Internal NAMESPACE rework, using pipette and AcidGenerics.

AcidExperiment 0.1.5 (2021-02-09)

Minor changes:

• Reworked the list of reexported functions. Now reexporting only from SummarizedExperiment and sessioninfo.

AcidExperiment 0.1.4 (2021-02-08)

Minor changes:

• Now reexporting some commonly used functions from SummarizedExperiment.

AcidExperiment 0.1.3 (2021-02-08)

Minor changes:

• sampleData: Bug fix for unwanted early return on minimal colData defined in SummarizedExperiment. This handling is required for downstream automatic plotting functions defined in AcidPlots, that make use of "sampleName" metadata column.

AcidExperiment 0.1.2 (2021-02-06)

Minor changes:

• Added ignoreVersion option to gene mapping functions.

AcidExperiment 0.1.1 (2021-02-06)

Major changes:

• Ensuring we're enforcing lower camel case naming conventions for metadata describing the columns slotted in colData.

Minor changes:

• Imported coercion methods from SummarizedExperiment.
• Added package.R, describing package info.

AcidExperiment 0.1.0 (2021-02-05)

Initial release, with code migrated from basejump package.

acidgenomics/r-acidexperiment documentation built on Jan. 17, 2024, 7:56 p.m.