tibble subclasses have been deemed unnecessary and have been removed from the package.
GRanges to a
valr compatible data.frame now uses the
gr_to_bed() function rather than
dplyr version < 0.8.0 is no longer supported due to unnecessary code bloat and challenges with handling multiple grouping structures (#359).
sort_by argument of
bed_random() has been changed to
sorted, and will now by default use
bed_sort() to sort the output, rather than rely on naming the sorting columns. Sorting can be suppressed by using
sorted = FALSE.
tbls processed by
bed_sort() no longer store either
sorted as attributes, due to these attributes being rarely checked in the codebase and potential sources of unexpected behavior.
Rcppfunctions have been reorganized to remove all dependencies on
Due to internal refactoring of Rcpp functions, only data.frames containing Numeric, Logical, Integer, Character, and List column types are supported. Columns containing Raw, Complex, or other R classes are not supported and will issue an error.
Factors are now disallowed from grouping variables in multiset operations to avoid sort order discrepancies, and compatibility with factor handling in
dplyr v.0.8.0. Factors will now be internally type-converted to character and a warning is issued.
as_tibble()only on non-tibble input, which prevents groups from being stripped from
Added new function,
bed_partition(), which is similar to
bed_merge() but collapses intervals to elemental intervals rather than the maximal overlapping region.
bed_partition() also can compute summaries of data from overlapping intervals. See examples in
bed_partition() and timings in
Several explicit comparisons to the Bioconductor GenomicRanges library are included for users considering using valr. See examples in
as.tbl_interval() and timings in
Update dplyr header files to v0.7
bed_intersect() and internal
intersect_impl were refactored to enable return of non-intersecting intervals.
The genome argument to
bed_makewindows() was deprecated and will produce a warning if used. Also error handling was added to check and warn if there are intervals smaller than the requested window size in
makewindows_impl() (#312 @kriemo)
bed_makewindows() now returns the number of windows specified by
num_win when the input intervals are not evenly divisble into
num_win, consistent with
bed_sort()has been de-deprecated to reduce
arrangecalls in library code.
bed_merge() (~4x), and
bed_flank() (~4x) (thanks to @kriemo and @sheridar). Thanks to the sponsors of the Biofrontiers Hackathon for the caffeine underlying these improvements.
bed_random()are now sorted properly.
Package dplyr v0.5.0 headers with valr to remove dplyr LinkingTo dependency.
tbl_genome() that wrap tibbles and enforce strict column naming.
trbl_genome() are constructors that take
tibble::tribble() formatting and
is.tbl_genome() are used to check for valid classes.
bed_random()are sorted by
src/init.c that calls
R_useDynamicSymbols to address NOTE in r-devel
Transfer repository to http://github.com/rnabioco/valr, update links and docs.
Move shiny app to new repo (http://github.com/rnabioco/valrdata).
Add Kent Riemondy to LICENSE file.