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Changelog

Source: NEWS.md

plyranges 1.31.5

  • added distance=TRUE option for join_overlap_*
  • added join_mcols_left(x,y) for GRanges x and tabular y

plyranges 1.27.6

  • added pull() method for Ranges objects that extracts a single column as a vector
  • moved dplyr to Depends and removing tidyverse reexports

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

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

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

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.