In this release, we are migrating some of the S4 generics previously exported in the bcbioBase package. We are consolidating these functions here for simplicity and stability.
prepareSummarizedExperiment, previously exported in the bcbioBase package. We are using the
makeprefix here for consistency (see other gene annotation functions).
curl::has_internetinternally to check for Internet connection. This applies to the annotation functions that query web databases.
SummarizedExperimentto an unstructured
list. This is the method used internally for
cleanSystemLibrary: Utility function to check whether a user has installed packages into the R system library. Refer to
.libPathsdocumentation for more information on library paths.
genomeBuildfor Ensembl annotation functions. The
genomeBuildargument still works but now will inform the user about the change.
prepareTemplatefrom bcbioBase package. Simplifed this function to copy all files inside
extdata/rmarkdown/sharedwithin a specified package. Currently in use for bcbioRNASeq, bcbioSingleCell, and the new pointillism clustering package.
makeGene2symbolFromGFFfunctions now support the
uniqueargument, which returns sanitized values in the
geneNamecolumn, ensuring there are no duplicates. This is enabled by default (recommended) but can be disabled using
unique = FALSE. This functionality was added to ensure consistent gene name handling in single-cell RNA-seq analyses.
basejump.save.compressglobal options, so the desired file type (e.g. RDS instead of RDA) and compression (e.g. xz instead of gzip) can be easily specified for an entire project.
sampleNamesnow supports assignment for
lanePatternregular expression pattern as a global, which was previously defined in the bcbioBase package.
ascoercion method support. Need to ensure
exportMethods(coerce)is included in
as(x, "tbl_df")won’t work when called from an Rscript without the package library loaded. Thanks @roryk for noticing this.
gene2symbolgeneric to use
..., since we’ve added the
unique = TRUEargument in this release.
annotable: Moved to
makeGRanges.Rfile, and improved the internal code to export supported formals also used in
makeGRangesFromEnsembl. The function should work exactly the same as previous releases, but now with clearer supported arguments in the documentation.
cleanSystemLibrary, since Travis CI installs packages into the system library, and causes this check to return
as(from, "tbl_df")for internal tibble coercion in all functions.
organismargument matching no longer suggests a default. The current list of supported organisms is in the documentation, and described in the internal
validObjectvalidity checks, where applicable.
sampleData: Made validity check stricter, requiring
sampleNamecolumn to be defined, otherwise the function will intentionally error.
formalsinternall to keep ggplot2 theme formals consistent.