v0.2.6

[mjsteinbaugh]

Major changes

• Added transform = TRUE argument to [ extraction method, allowing the user to skip automatic [DESeq2][] transformations, which can be CPU intensive for large datasets.
• Switched back to using plotMA() instead of plotMeanAverage(). An MA-plot by definition is not a "Mean Average" plot, so this function name is misleading. We will keep the plotMeanAverage() working but it is now soft deprecated.
• plotGeneSaturation() now supports label argument, similar to plotPCA().

Minor changes

• Improved internal handling during tximport() call to handle transcript version mismatch with tx2gene data.frame. This can result if the bcbio pipeline is using an old genome build.
• Ensure genomeBuild is detected from [AnnotationHub][] rowRangesMetadata if applicable, and not left NULL in the metadata.
• Updated internal code to use aes() instead of aes_string(), which uses [tidyeval][] and quasiquotation.
• plotGene(): reduced the number of return options to simply "facet" and "wide". Previously, this also supported "grid", "list", and "markdown", but these were removed because they are not frequently used.
• plotGene(): Switched back to internal lapply() call instead of using BiocParallel::bplapply(). This doesn't always work perfect in an HPC environment (e.g. HMS O2 cluster).
• Soft deprecated plotMeanAverage() in favor of plotMA().
• All S4 generics with method support are exported for easier lookup in the reference documentation.
• All function reexports have been consolidated in [bcbioBase][] package.

[codecov[bot]]

Codecov Report

Merging #113 into master will increase coverage by 12.51%. The diff coverage is 97.01%.

@@             Coverage Diff             @@
##           master     #113       +/-   ##
===========================================
+ Coverage   85.72%   98.23%   +12.51%     
===========================================
  Files          44       45        +1     
  Lines        2256     2272       +16     
===========================================
+ Hits         1934     2232      +298     
+ Misses        322       40      -282

Impacted Files	Coverage Δ
R/topTables-methods.R	100% <ø> (ø)
R/aggregateReplicates-methods.R	100% <ø> (ø)
R/tmm-methods.R	100% <ø> (ø)
R/nonzeroGenes-internal.R	100% <ø> (ø)
R/alphaSummary-methods.R	100% <ø> (ø)
R/plotDispEsts-methods.R	100% <ø> (ø)
R/ggplot2-internal.R	100% <ø> (ø)
R/plotMeanSD-methods.R	100% <ø> (ø)
R/melt-internal.R	100% <ø> (ø)
R/AllGenerics.R	100% <ø> (ø)	:arrow_up:
... and 65 more

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