NEWS.md

In sa-lee/plyranges: A fluent interface for manipulating GenomicRanges

plyranges 1.9.3

• minor spelling and layout fixes to vignette,
• @PeteHaitch corrected table layout in vignette

plyranges 1.9.2

• minor documentation fixes

plyranges 1.9.1

• Spencer Nystrom has made several significant contributions to the join_nearest family of functions:

  1. join_nearest_(x, y, ..., distance = TRUE) family of functions now takes a new argument, distance, which allows the user to add a column for the distance of the nearest range y to that in x.
  2. add_nearest_distance_(x, y, ...) family of functions, which will add a new metadata column to the x ranges object which contains the distance to its nearest neighbor in y. If there are no nearest neighbors, the new column will be given a missing value.

plyranges 1.7.16

• refactoring of select internals, improved speed when casting a GRanges -> DataFrame

plyranges 1.7.15

• further fixes to reduce/disjoin internals

plyranges 1.7.14

• fixes reduce/disjoin internals cleans up disjoin cases when an expansion occurs

plyranges 1.7.13

• set tidyselect version to be v 1.0
• set coverage method for delegating ranges
• fix docs for bam reading

plyranges 1.7.11

• move from tidyselect::vars_select() to tidyselect::eval_select()

plyranges 1.7.7

• update handling of list columns, expand_ranges() no longer takes cartesian product if lists are parallel. summarize() properly handles list column output without blowing out number of columns.

plyranges 1.7.6

• adds method for dplyr::sample_n()

plyranges 1.7.5

• fixed issue #62 for Ranges construction, the as_granges() and as_iranges() functions now handle List columns correctly
• added in helper functions for dealing with names in Ranges. See ?ranges-names for details.

plyranges 1.7.4

• added slice() for Ranges, and GroupedRanges
• internals of grouping have been overhauled, but there shouldn't be any user facing changes. It is now much faster to generate groupings.
• group information can be interrogated with dplyr::group_keys()
• a GRangesList can be obtained automatically from a GroupedGenomicRanges with dplyr::group_split()
• group indices can be generated with dplyr::group_indices()

plyranges 1.7.3

• shift_downstream() and shift_upstream() now properly handle vector amounts of shift. Fixes issue #73

plyranges 1.7.2

• Left outer join overlap operations now work if either x or y have no metadata columns see #70
• Left outer join overlap operations will also correctly behave in situations when there are no non-overlapping ranges.
• Left outer join overlaps no longer modify seqinfo (see here)[https://support.bioconductor.org/p/125623/]
• patch left outer join when x or y are IRanges, flesh out overlaps documentation.

plyranges 1.7.1

• Reformatting NEWS.md so no longer softlinks to inst/NEWS

plyranges 1.5.13

• plyranges release and devel have removed unnest() and replaced it with expand_ranges() due to changes in the tidyr API. Please replace all uses of this function with expand_ranges()

plyranges 1.3.4

• fixed bind_ranges so it preserves rownames

plyranges 1.1.5

• enable right generics to be called upon invoking plyranges functions without loading plyranges

plyranges 1.1.4

• added tile/window methods
• fixed up documentation

plyranges 1.1.3

• doc updates

plyranges 1.1.2

• speed up of group_by methods
• refactor of BAM reading utilities

plyranges 0.99.10

• refactored set_width out so it's called internally by mutate
• along with set_width there are other internal set_ methods
• add _within_directed variants for overlaps methods
• modified overscope_ranges to be an S3 method, should enable more refactoring in the future

plyranges 0.99.9

https://bioconductor.org/packages/devel/bioc/html/plyranges.html

• package passed review and is now on Bioconductor devel branch!
• I've been pretty slack with updating the NEWS file but will be more diligent in the future.

sa-lee/plyranges documentation built on April 15, 2024, 12:25 p.m.