This release is the beginning of an attempt to rework the basejump codebase a bit and make the package easier to unit test on Travis CI. bcbio R packages will be pinned to v0.7.2 during this development period.
Here we are working to split out the functionality of basejump into several, smaller sub-packages:
Migrating some additional base code that can be dispatched on either
SingleCellExperiment from the bcbio R packages. We’re going to split out some of the single-cell RNA-seq functionality into separate packages, since a lot of my work moving forward deals with the 10X Genomics Cell Ranger platform, rather than the bcbio-supported inDrops platform.
plotPCAcode from bcbio R packages.
formalsListglobal variable, which stashes
getOptiondefaults used in some functions, namely the save/load functions and some plotting functions.
formalsdeclaration internally to make the parameters more consistent across functions.
assertthat::validate_thatin S4 class validity checks. Removed former approach using internal
interestingGroupsdoesn’t attempt validity check using
validObjectby default, which can be enabled instead using
check = TRUE.
sampleData: Tightened up internal assert checks.
PANTHER: Minor tweaks to internal variable names inside
transmit: Improved messages. Temporarily disabled working example, since it consistently fails on Travis CI.
autopadZeros. Useful for padding zeros inside of a character vector.
basenameSansExt. Quickly get the basename without the file extension for desired file path(s). Surprisingly, this isn’t defined in the tools package so I wrote my own.
cleanSystemLibrary. I ran into some shared library configuration issues on the Azure infrastructure, so this utility function is useful for checking wheter an R installation has a clean library.
plotGenderMarkers: Migrated the
SummarizedExperimentmethod from bcbioRNASeq package.
autopadZeros: Improved internal code to keep track of names for
charactermethod. Also added method support for
SummarizedExperiment, which works on the column names (e.g. sample names) only by default.
Ensembl2Entrez: Simplify validity check to require
entrezIDcolumn. Also reworked and improved internal code that supports run-length encoding (Rle) using
export: Improved documentation for
makeGRangesFromEnsembl: Improved messages to user.
plotCountsPerBiotype: Improved error messages for when the biotype isn’t defined.
plotPCA: Add support for unique sample detection with
areSamplesUnique, similar to the approach used in the bcbioRNASeq quality control R Markdown.
humanize. New generic that enables easy conversion to human-friendly column and/or row names. Useful for CSV file export in particular.