Version 0.3

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 0.3.1 (2020-08-07)

Minor changes:

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

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 0.3.3 (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 0.3.4 (2020-08-18)

New functions:

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

DESeqAnalysis 0.3.5 (2020-08-18)

Minor changes:

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

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 0.3.7 (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 0.3.8 (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 0.3.9 (2020-10-08)

Minor changes:

• Updated package dependency version requirements.

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 0.3.11 (2021-02-10)

Minor changes:

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

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.