selectSamples. These functions are now deprecated here in basejump (see
deprecated.Rfile for more information).
revcomphave been deprecated in favor of
reverseComplementfrom the Biostrings package.
warn, in place of
loadData. Additionally, the file name must match the internal name in the RData file, otherwise
loadDatawill warn the user. This is more strict than the default behavior of
base::load, but helps prevent accidental overwrite in the current working environment.
localOrRemoteFile, previously an internal function, is now exported.
annotablenow uses internal GRCh37 annotations from the annotables package, which is saved in the
extdata/directory internally. Previously, these genome annotations were accessed from lazy loaded data saved in the
data/directory of the package repository.
annotablesnow checks for all packages attached by ensembldb and AnnotationHub and forces detachment at the end of the function call. Otherwise, this can result in the unwanted effect of ensembldb masking other user-loaded functions, such as the tidyverse suite (e.g.
camelnow handles delimited numbers a little differently. Previously, delimiters in between numbers (e.g. the commas in “1,000,000”) were stripped. Sometimes this can result in confusing names. For example, if we have a column formatted in dotted case containing a decimal (e.g. “resolution.1.6”), the decimal would be stripped (e.g. “resolution16” in camel). Now, we sanitize a numeric delimiter as a lower case “x” character (e.g. “resolution1x6”). This ensures that numbers containing decimals remain semantically meaningful when sanitized with
grepl) calls have been simplified to use the default order of “pattern, replacement, x”.
convertTranscriptsToGenesfunctions. Previously some of this functionality was contained within the
tx2genegenerics for the character method. This behavior was inconsistent with
tx2geneusage in the bcbio R packages, so I decided to split these out into separate functions. Now
tx2genework consistently with the
annotablefunction to return gene-to-symbol and transcript-to-gene identifier mappings in a
markdownPlotlistare now exported as S4 generics. The
md*function variants are now exported as aliases.
geomeanhas been renamed to