Changelog 0.3

bcbioRNASeq 0.3.0 (2018-11-06)

Development fork of hbc/bcbioRNASeq. Code development will proceed here on the fork until a stable release is ready to merge back at official HBC repo, to avoid any disruption for active RNA-seq experiments.

New S4 classes

• Added new DESeqAnalysis S4 class, which helps containerize up a DESeq2 analysis, often requiring corresponding DESeqDataSet, DESeqTransform, and DESeqResults objects. Note that this class may be defined in a separate package in a future update.

Code migration to basejump

• aggregateReplicates has moved to basejump, and now works primarily on SummarizedExperiment method, instead of bcbioRNASeq.
• Offloaded a number of S4 generics to basejump infrastructure, which are now defined in the bioverbs package: alphaSummary, contrastName, plot5Prime3PrimeBias, plotCountDensity, plotCountsPerGene, plotDEGHeatmap, plotDEGPCA, plotExonicMappingRate, plotGenderMarkers, plotGeneSaturation, plotGenesDetected, plotIntronicMappingRate.
• metrics method, which returns a tbl_df of colData, has been moved to basejump.
• plotCorrelationHeatmap code is now primarily defined in basejump as a SummarizedExperiment method. bcbioRNASeq now calls this method internally but keeps support for normalized counts argument.
• Removed tpm method support, which is now handled by SummarizedExperiment method support in basejump.

S4 method reworks

• Reworked internal code, splitting out S4 methods into internal functions (e.g. counts.bcbioRNASeq). This step is recommended by Bioconductor, and can make troubleshooting easier.
• export: Reworked S4 methods for DESeqResults and DESeqResultsTables S4 classes.
• extract (i.e. [) method: Switched transform formal to recalculate. Added additional assert checks. Operation no longer changes the saved version of bcbioRNASeq, slotted into metadata.
• interestingGroups formal is now set NULL instead of missing for plotting functions.
• markdown: Initial support of new S4 generic, which returns a markdown table of sample metadata.
• plot5Prime3PrimeBias: Added an addition grep matching step to handle differential variations on the x5x3Bias column in colData.
• plotCountDensity S4 method has been removed. Use plotGeneSaturation generic with geom = "density" argument instead.
• plotCountsPerBiotype: New S4 method support, which calls basejump SummarizedExperiment method.
• plotDEGHeatmap: Draft update of DESeqResults method.
• plotDEGPCA: Draft update of DESeqResults method.
• plotDispEsts: Split out and reworked internal method definition.
• plotGenesDetected: This code has been moved to basejump and is now defined against SummarizedExperiment.
• plotMA: Reworked internal DESeqResults method code. Added draft support for new DESeqAnalysis S4 class. Keeping plotMeanAverage reexported, since this function is used in the F1000 workflow paper.
• plotMappingRate: Set the default limit back down to 0.7.
• plotMeanSD: Reworked internal DESeqDataSet code. Added additional assert checks and changed the default handling of vst and rlog internal formals.
• plotPCA: Draft update of SummarizedExperiment. Will offload this code to basejump in a future update. Switched return argument to support tibble and S4 DataFrame – note change from previous support for data.frame.
• Deleted plotPCACovariates method, since DEGreport is failing. Will add back support for this generic in a future update.
• plotQC: Initial method support for bcbioRNASeq.
• plotTotalReads: Reworked and tightened up internal ggplot2 code.
• plotVolcano: Draft update to DESeqResults method. Will rework this code with a DESeqAnalysis approach in a future update.
• relativeLogExpression: Added S4 method support.
• resultsTables: Removed this approach to subsetting DESeqResults. This will be a rework in the upcoming DESeqAnalysis package.
• sampleData: Simplified internal code, which takes advantage of updates to SummarizedExperiment defined in basejump.
• updateObject: Reworked internal metadata handling.

Example data reorganization

• Renamed and simplified example datasets. Now only exporting bcb (bcbioRNASeq) and deseq (DESeqDataSet) examples.
• bcb_small, dds_small, gender_markers, and res_small have been removed.
• Updated and consolidated corresponding data-raw/ scripts.
• Reworked internal extdata/bcbio/ example datasets. Testing out both 2017-05-23_rnaseq and 2018-03-18_GSE67267-merged data.

R Markdown templates

• Stripped down supported R Markdown templates. Currently simplified code base to support Quality Control markdown (quality_control). Differential expression and functional analysis templates have been temporarily removed but will be re-added in the future.

Minor changes

• Reorganized S4 class definitions and validity checks in AllClasses.R. Previously, this code was split out per S4 (e.g. bcbioRNASeq-validity.R).
• Moved S4 coercion methods from coerce-methods.R to as-methods.R.
• Added internal assert checks in assert-internal.R.
• Consolidated internal DESeq2 code into DESeq2-internal.R.
• Consolidated and defined additional global variables into globals.R.
• Reorganized internal .meltCounts code.
• Consolidated global package parameter arguments into params.R.
• bcbio prefix has been renamed to basejump, where applicable. Refer to global function params defined with getOption, and internal ggplot2 utility functions, such as basejump_geom_abline.
• Draft support for countsFromAbundance selection in internal tximport call. This is useful for some transcript-level analyses.

Deprecations

• Removed defunct download function.
• New deprecations: plotCountDensity, plotPCACovariates, resultsTables.

bcbioRNASeq 0.3.1 (2018-11-14)

Major changes

• Improved validity method for bcbioRNASeq S4 class.
• extract ([) method: Improved internal handling of rowRanges and colData. Now using I internally for complex S4 columns in mcols for rowRanges.
• Reworked imports back to basejump instead of attempting to use subpackages: basejump.annotations, basejump.assertions, basejump.classes, basejump.coerion, basejump.developer, basejump.experiment, basejump.generics, basejump.globals, basejump.io, basejump.markdown, basejump.plots, basejump.sanitization. Rethink this approach in a future update.

Minor changes

• Resaved example bcb dataset.
• Miscellaneous internal assert check fixes and updates.
• Miscellaneous documentation improvements.
• Added internal Rle global variable. May want to avoid this approach because Rle is a defined function in S4Vectors, however.
• Offloaded some global documentation params to basejump.
• Reworked some global params set by getOption in formals.

bcbioRNASeq 0.3.2 (2018-11-19)

Major changes

• Splitting out new DESeqAnalysis S4 class to a separate package.

Deprecated functions and methods

• Functions removed from NAMESPACE: magrittr pipe (%>%), DESeqAnalysis, DESeqResultsTables, alphaSummary, contrastName, export, markdown, plotDEGHeatmap, plotDEGPCA, plotMA, plotMeanAverage, plotVolcano, topTables.
• alphaSummary: Migrated DESeqDataSet method to DESeqAnalysis package.

Example data

• Deleted deseq example, which has migrated to DESeqAnalysis package.

Minor changes

• Reorganized internal assert checks.
• Miscellaneous documentation improvements.
• Improved consistency of global formals (using getOption) via formalsList global variable.

bcbioRNASeq 0.3.3 (2018-11-25)

Minor changes

• Added additional library loads to _setup.R: rmarkdown, basejump, DESeq2.
• plotGene: Updated working example.
• Improved reexport of sampleData<- generic.
• Updated Travis CI configuration.

bcbioRNASeq 0.3.4 (2018-11-29)

Major changes

• Improved and simplified quality control template. Removed Dropbox mode (which may be added back in a future update). Identical samples detection is now supported automatically in the plotting functions, which was previously defined in the QC template.
• Improved subset sample handling inside extraction method. Extraction method now imports useful relevelRowRanges and relevelColData utilities from basejump.

Minor changes

• Removed sampleData<- reexport.
• Documentation fixes and improvements, particularly to the bcbioRNASeq generator function.
• Reworked internal gffFile handling inside bcbioRNASeq generator function.
• Simplified passthrough in internal .new.bcbioRNASeq call.
• plot5Prime3PrimeBias now uses color argument instead of fill.
• plotDispEsts now checks for duplicate samples and early returns.
• Consistently use British spelling variants (colour instead of color) for ggplot2 functions. Our formals will stick with American English though.
• plotTotalReads: Bumped recommended default to 20 million from 10 million.

bcbioRNASeq 0.3.5 (2018-12-01)

Major changes

• Added additional improvements to quality control template. Ensuring that setup chunk never caches. bcbioRNASeq object should be called using params$object_file. This convention will be used across all other bcbio R packages. Reworked and simplified plotCountsPerGene section of QC template.

Minor changes

• Added early return method for objects without modification extract method. Might want to reconsider this approach if the user just wants to reorder samples. We’re checking for unmodified return by looking for identical raw counts matrix before and after extraction call.
• plotCountsPerBiotype: Ensure normalized argument uses “tpm” first.
• plotDispEsts: Switch to using hasUniqueCols internally instead of areSamplesUnique.

bcbioRNASeq 0.3.6 (2018-12-12)

This is the first release that switched over to using [goalie][] for assert checks instead of [assertive][].

Major changes

• bcbioRNASeq generator has been overhauled to use assert for assert checks.

Minor changes

• Ensure title is quoted in R Markdown.
• Switched to using validate in place of validate_that in validity checks.
• Miscellaneous documentation improvements.
• Now using match.arg internally to check validity of countsFromAbundance argument passthrough to tximport.

bcbioRNASeq 0.3.7 (2019-01-13)

Major changes

• Overhauled validity method for bcbioRNASeq. Improved check steps using ok method, similar to approach in [goalie][].
• Added back plotPCACovariates method support.

Minor changes

• Updated pkgdown configuration. Removed alphaSummary, contrastName, export, markdown, sampleData, topTables
• [goalie][] package has been updated to support nullOK mode where applicable. This is particularly use for formals that use NULL by default. See bcbioRNASeq generator changes, for example.
• prepareRNASeqTemplate example is causing build checks to fail, so disable.
• Improved CI configuration.

bcbioRNASeq 0.3.8 (2019-01-17)

Minor changes

• .tximport: Use makeNames to check for valid names internally.
• Removed FIXME comment and improved documentation.
• Travis CI configuration fixes to get build checks to pass.

bcbioRNASeq 0.3.9 (2019-01-23)

Minor changes

• Bug fixes for interestingGroups handling in plotting functions. Needed to add back an interestingGroups<- assignment call to slot the object.
• Removed sanitizeRowData and sanitizeSampleData from imports.

bcbioRNASeq 0.3.10 (2019-02-01)

Minor changes

• Travis CI build configuration and documentation fixes.

bcbioRNASeq 0.3.11 (2019-02-12)

Minor changes

• Renamed plotGene to plotCounts, to match consistency in basejump and DESeqAnalysis package updates.
• Updated dependencies to provide improved backwards compatibility support for R 3.4 / Bioconductor 3.6.

bcbioRNASeq 0.3.12 (2019-03-18)

Major changes

• sampleData: Moved method support to basejump package.

Minor changes

• Resaved example data.
• Sample metadata chunk in quality control template now returns DataFrame.
• Improved some deprecation messages.
• CI configuration improvements.

bcbioRNASeq 0.3.13 (2019-03-29)

Minor changes

• Added additional checks to bcbioRNASeq validity method.
• Draft update to quality control template, to support parameterized bcbioRNASeq object input. This is likely not necessary and will be removed in a future update.
• Added additional checks for bcbioRNASeq to DESeqDataSet coercion.
• Improved internal perMillion argument code handling inside plotting functions: plotMappedReads, plotTotalReads.
• Removed reexports.R. No longer reexporting Gene2Symbol or magrittr pipe.

bcbioRNASeq 0.3.14 (2019-04-01)

Moved forked development repository to [Acid Genomics][].

Major changes

• Switched unit testing data URL from seq.cloud to acidgenomics.com.

Minor changes

• Reworked internal reexports for assignment generics. See counts for example.
• Miscellaneous documentation improvements.
• Switched from basejump prefix to acid, where applicable.
• Reexported essential functions from basejump required for QC template to render without basejump being attached.

bcbioRNASeq 0.3.15 (2019-04-11)

Minor changes

• Ensuring that all basejump functions necessary for the quality control template get reexported.
• Renamed R Markdown template files and travis-render.sh script into kebab case, rather than snake case.
• Documentation improvements (using inheritParams).

bcbioRNASeq 0.3.16 (2019-04-17)

Minor changes

• Tweaks to quality control template.
• Switched Travis CI configuration to use rnaseq Docker image.

bcbioRNASeq 0.3.17 (2019-04-22)

Minor changes

• Bar plots now show the first sample at the top of the Y axis when flip = TRUE. This is more human readable.
• Quality control template now uses bcbiornaseq_file as main input param.
• Bug fix: added back internal .normalizedTrans function required for some quality control plots.

bcbioRNASeq 0.3.18 (2019-04-25)

Minor changes

• S4 generic reexport documentation fixes.

bcbioRNASeq 0.3.19 (2019-05-05)

Major changes

• Now pinned to R >= 3.5.

Minor changes

• Improved Travis CI and AppVeyor CI configuration.

bcbioRNASeq 0.3.20 (2019-05-29)

Minor changes

• Added support for size factor adjusted counts as “sf” in counts call.
• Improved internal trans axis labeling handling for DESeqTransform counts.
• plotMeanSD: Improved default colors. Improved internal non-zero count handling. Reworked plot headers.

bcbioRNASeq 0.3.21 (2019-07-17)

Major changes

• Initial support for bcbioRNASeq to DGEList (edgeR) object coercion.
• relativeLogExpression: Improved internal code, using edgeR calcNormFactors approach.

Minor changes

• Updated basejump dependency to v0.10.11.
• Improved Travis CI docker config to check coverage and lints.
• Improved Bioconductor installation instructions.

bcbioRNASeq 0.3.22 (2019-07-23)

Major changes

• bcbioRNASeq: Now supporting fast argument, which enables the user to skip any internal DESeq2 calculations. This will skip generation of normalized, vst, and fpkm matrices. Note that automatic rlog matrix generation is no longer supported, since it’s often too slow, especially for large datasets. If you want to generate rlog counts, simply coerce the bcbioRNASeq object to a DESeqDataSet, then run the rlog function.
• Aligned counts are now saved inside the object when a pseudoaligner (e.g. salmon, kallisto) are used to define the primary counts assay. These values are saved in an aligned matrix.

New functions

• pseudoVsAligned: Visually inspect the correlation of pseudoaligned counts to the aligned counts. Note that default bcbio genomes use legacy UCSC builds, where as the pseudoaligners generate values from newer Ensembl transcript annotations.

Minor changes

• Updated package dependency versions.

bcbioRNASeq 0.3.23 (2019-07-29)

Major changes

• updateObject: Worked internal approach to be compatible with upcoming Bioconductor 3.10 release. Has to rethink the strategy to handling assays internally, which can no longer be easily coerced from assays slot in the bcbioRNASeq object, due to changes in ShallowSimpleListAssays handling. This should return an object in exactly the same manner as previous releases.

bcbioRNASeq 0.3.24 (2019-08-12)

Minor changes

• Simplified internal object creation in bcbioRNASeq, [, and updateObject.
• Improved message consistency.

bcbioRNASeq 0.3.25 (2019-08-20)

Major changes

• Made subsetting factor for extract ([) operations.
• updateObject: Improved rowRanges handling.

Minor changes

• bcbioRNASeq generator now captures call using standardizeCall instead of match.call, and automatically expands all default arguments.
• Improved NAMESPACE and basejump dependencies.
• Made vsn and DEGreport packages optional, to reduce the number of dependencies required for installation.
• plotPCACovariates: Reworked internal code to not depend on dplyr.
• Removed internal code dependencies on magrittr pipe.

bcbioRNASeq 0.3.26 (2019-08-27)

Minor changes

• Now requiring R 3.6, as we near a candidate Bioconductor release.
• Updated basejump dependencies.

bcbioRNASeq 0.3.27 (2019-09-09)

Minor changes

• bcbioRNASeq: Internal generator now calls importSampleData using pipeline = "bcbio" argument, so we don’t run into breaking changes when handling user metadata in a future basejump update.
• Updated basejump dependency versions.

bcbioRNASeq 0.3.28 (2019-09-17)

Minor changes

• Reworked quality control plots to use “labels” instead of “title”.
• Updated R Markdown templates and added render code coverage in testthat-extra.
• Updated vignette to use shared bibliography.bib file from basejump.

bcbioRNASeq 0.3.29 (2019-10-30)

Minor changes

• Added support for Bioconductor 3.10.
• Updated internal DataFrame validity checks to also check for DFrame class, which has changed in latest S4Vectors 0.23 release.
• Updated basejump dependency versions.