Changelog 0.1

bcbioRNASeq 0.1.0 (2017-10-23)

  • Updated version and author information to match the F1000 Research workflow.
  • Added an f1000v1 branch containing the reproducible code used to generate the figures in our workflow.
  • Modified plotMA to support vertical or horizontal layout return. Also added an argument to remove the color legend, which is typically not that informative.
  • Added custom color palette support to the quality control functions.
  • Upgrading from bcbioRNADataSet (< 0.1.0) to bcbioRNASeq class object is now possible using as coercion method.
  • Object oriented methods are now restricted to use bcbioRNASeq object. Legacy bcbioRNADataSet objects must be upgraded to bcbioRNASeq class.

bcbioRNASeq 0.1.1 (2017-10-26)

  • Added support for coloring of multiple interesting groups in quality control plots.

bcbioRNASeq 0.1.2 (2017-11-08)

  • Updated package imports to match Bioconductor 3.6.
  • Added support for interesting groups assignment with interestingGroups<-.
  • Renamed plotGeneHeatmap to simply plotHeatmap.
  • Added gender marker support for Homo sapiens.
  • Improved support for multiple interesting groups in quality control plots. Now interestingGroups is defined as a column in the metrics data.frame that is used to specify the plot color/fill. This matches the convention in the bcbioSingleCell 0.0.22 update.
  • Sample metadata columns are now consistently set as factors.

bcbioRNASeq 0.1.3 (2017-12-03)

  • Combined examples (bcb, dds, res, etc.) into a single examples object. This helps avoid accidental use of example bcb in an analysis.
  • Moved ggplot imports from internal-ggplot.R to above each function.
  • Renamed maxSamples parameter in loadRNASeq to transformationLimit. If there are more samples than this limit, then the DESeq2 transformations will be skipped. In this case, rlog and vst will not be slotted into assays.
  • Added a colData sanitization step in loadRNASeq to ensure rows are in the same order as the columns in the counts matrix. Otherwise, DESeq will report an error at the DESeqDataSetFromTximport step. We’re also ensuring the factor levels get updated here.
  • Now using glimpse instead of str in examples, where applicable.
  • Added colData<- assignment method support. This requires a DataFrame class object. Upon assignment, the internal colData at bcbio(object, "DESeqDataSet"), assays(object)[["rlog"]] and assays(object)[["vst"]] are also updated to match.
  • Initial assignment support for design, which will update the internal DESeqDataSet.
  • Added method support for gene2symbol generic, which will now return a 2 column data.frame with ensgene and symbol columns. This is helpful for downstream gene to symbol mapping operations.
  • Added working example for interestingGroups<- in the documentation.
  • Added some code to improve factor releveling, where applicable. See internal-meltLog10.R for example.
  • Now explicitly defining the custom color palettes (e.g. viridis::scale_fill_viridis(discrete = TRUE). This makes it clearer to the user in the documentation where these palettes are located.
  • Improved axis label support in plotGene.
  • plotHeatmap now uses internal gene2symbol mappings from stashed annotable, instead of always querying Ensembl. The user can define custom mappings with the gene2symbol argument, if desired.
  • plotPCA now supports custom color palettes. The shapes parameter has been removed because it doesn’t work well and is limited to datasets with few samples. This behavior matches the PCA functionality in DESeq2.
  • Improved internal code for plotVolcano. Added support for gene2symbol argument, like in plotHeatmap. If left missing, the function will query Ensembl for the gene2symbol mappings. We’re now using data instead of stats as the main data source.
  • Improved legibility of subset method code.
  • Added some additional reexports, which are used for the package documentation and website.
  • Simplified legacy object coercion method code.
  • Updated Bioconductor installation method code. We’re now using the dependencies argument, which allows for automatic install of suggested packages along with imports.

bcbioRNASeq 0.1.4 (2018-11-27)

  • Migrated all basejump function imports to bcbioBase package.

bcbioRNASeq 0.1.5 (2018-01-31)

  • Import shared dependency functions from bcbioBase instead of basejump.
  • Added method support for selectSamples.
  • organism and genomeBuild parameters are now user-definable in the main loadRNASeq import function.
  • Fixed gene subsetting method on S4 object, which handles genes using intersect in the featureCounts matrix.
  • Removed internal aggregateReplicates code. This needs to be reworked and added back in a future release.
  • Improve method for handling a missing normalized counts matrix in the assays slot. This can occur when the user opts to skip the CPU-intensive DESeq2 normalizations.
  • Improved internal code for the quality control functions. Improved the if statements to be more class specific.
  • Renamed plotCorrelationHeatmap transform argument to normalized, for consistency with the counts generic.
  • Added title support to plots, where applicable.
  • Updated internal code for plotDEGHeatmap.
  • Updated internal marker handling code for plotGenderMarkers.
  • resulsTables function now defaults to summary = TRUE.

bcbioRNASeq 0.1.6 (2018-02-20)

  • Bug fix for gene-to-symbol mappings in plotDEGHeatmap.
  • Added support for quickly plotting differentially expressed genes (DEG) in a PCA plot with plotDEGPCA.
  • Added support for Dropbox shared links to resultsTables, for use with the Stem Cell Commons database.
  • Added assert checks internally for all functions.
  • Improved internal code for plotGene and plotGenderMarkers to run faster.
  • Deprecated data frame methods based on metrics for QC functions.

bcbioRNASeq 0.1.7 (2018-02-28)

  • Bug fix for [ subset method dropping metrics in metadata.
  • Simplified unit testing for Dropbox mode enabled in resultsTables.

bcbioRNASeq 0.1.8 (2018-04-03)

  • Bug fix for gene2symbol argument not renaming rows in plotDEGHeatmap.