as.tbl_interval()
to call as_tibble()
only on non-tibble input, which prevents groups from being stripped from tibble()
input (#338).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 vignette('benchmarks')
@kriemo.
Several explicit comparisons to the Bioconductor GenomicRanges library are included for users considering using valr. See examples in as.tbl_interval()
and timings in vignette('benchmarks')
.
All relevant tests from bedtool2 were ported into valr. Bugs identified in corner cases by new tests were fixed (#328 @raysinesis)
bed_jaccard()
now works with grouped inputs (#216)
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)
Fixed off by one error in reported distances from bed_closest()
. Distances reported now are the same as bedtools closest
behavior (#311).
bed_glyph()
accepts trbl_intervals
named other than x
and y
(#318).
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 bedtools
behavior.
The output of findOverlaps()
is now sorted in subtract_impl()
to prevent reporting intervals that should have been dropped when calling bed_subtract()
(#316 @kriemo)
A manuscript describing valr has been published in F1000Research.
New S3 generic as.tbl_interval()
converts GenomicRanges::GRanges
objects to tbl_interval
.
New create_tss()
for creating transcription start sites.
Improve documentation of interval statistics with more complex examples.
bed_sort()
has been de-deprecated to reduce arrange
calls in library code.bed_merge()
now reports start/end columns if spec is provided (#288)New create_introns()
, create_utrs5()
and create_utrs3()
functions for generating features from BED12 files.
Speed-ups in bed_makewindows()
(~50x), 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.
bed_intersect()
now accepts multiple tbls for intersection (#220 @kriemo).
new tbl_interval()
and tbl_genome()
that wrap tibbles and enforce strict column naming. trbl_interval()
and trbl_genome()
are constructors that take tibble::tribble()
formatting and is.tbl_interval()
and is.tbl_genome()
are used to check for valid classes.
bed_random()
are sorted by chrom
and start
by default.bed_jaccard()
and use numeric values for calculation (fixes #204).bed_sort()
in favor of using dplyr::arrange()
explicitly (fixes #134).add src/init.c
that calls R_registerRoutines
and R_useDynamicSymbols
to address NOTE in r-devel
Deprecate dist
parameter in bed_closest()
in favor of using user supplied functions (#182 @kriemo)
Make .id
values sequential across chroms in bed_cluster()
output (#171)
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.
bed_merge()
now merges contained intervals (#177)test / vignette guards for Suggested RMySQL
fixed memory leak in absdist.cpp
fixed vignette entry names