valr
provides tools to read and manipulate genome intervals and signals, similar to the BEDtools
suite. valr
enables analysis in the R/RStudio environment, leveraging modern R tools in the tidyverse
for a terse, expressive syntax. Compute-intensive algorithms are implemented in Rcpp
/C++, and many methods take advantage of the speed and grouping capability provided by dplyr
.
The latest stable version can be installed from CRAN:
install.packages('valr')
The latest development version can be installed from github:
# install.packages("devtools")
devtools::install_github('rnabioco/valr')
Why another tool set for interval manipulations? Based on our experience teaching genome analysis, we were motivated to develop interval arithmetic software that faciliates genome analysis in a single environment (RStudio), eliminating the need to master both command-line and exploratory analysis tools.
Note: valr
can currently be used for analysis of pre-processed data in BED and related formats. We plan to support BAM and VCF files soon via tabix indexes.
The functions in valr
have similar names to their BEDtools
counterparts, and so will be familiar to users coming from the BEDtools
suite. Unlike other tools that wrap BEDtools
and write temporary files to disk, valr
tools run natively in memory. Similar to pybedtools
, valr
has a terse syntax:
library(valr)
library(dplyr)
snps <- read_bed(valr_example('hg19.snps147.chr22.bed.gz'), n_fields = 6)
genes <- read_bed(valr_example('genes.hg19.chr22.bed.gz'), n_fields = 6)
# find snps in intergenic regions
intergenic <- bed_subtract(snps, genes)
# find distance from intergenic snps to nearest gene
nearby <- bed_closest(intergenic, genes)
nearby %>%
select(starts_with('name'), .overlap, .dist) %>%
filter(abs(.dist) < 5000)
#> # A tibble: 1,047 x 4
#> name.x name.y .overlap .dist
#> <chr> <chr> <int> <int>
#> 1 rs530458610 P704P 0 2579
#> 2 rs2261631 P704P 0 - 268
#> 3 rs570770556 POTEH 0 - 913
#> 4 rs538163832 POTEH 0 - 953
#> 5 rs190224195 POTEH 0 -1399
#> 6 rs2379966 DQ571479 0 4750
#> 7 rs142687051 DQ571479 0 3558
#> 8 rs528403095 DQ571479 0 3309
#> 9 rs555126291 DQ571479 0 2745
#> 10 rs5747567 DQ571479 0 -1778
#> # ... with 1,037 more rows
valr
includes helpful glyphs to illustrate the results of specific operations, similar to those found in the BEDtools
documentation. For example, bed_glyph()
illustrates the result of intersecting x
and y
intervals with bed_intersect()
:
library(valr)
x <- trbl_interval(
~chrom, ~start, ~end,
'chr1', 25, 50,
'chr1', 100, 125
)
y <- trbl_interval(
~chrom, ~start, ~end,
'chr1', 30, 75
)
bed_glyph(bed_intersect(x, y))
valr
can be used in RMarkdown documents to generate reproducible work-flows for data processing. Because computations in valr
are fast, it can be for exploratory analysis with RMarkdown
, and for interactive analysis using shiny
.
Remote databases can be accessed with db_ucsc()
(to access the UCSC Browser) and db_ensembl()
(to access Ensembl databases).
# access the `refGene` tbl on the `hg38` assembly
ucsc <- db_ucsc('hg38')
tbl(ucsc, 'refGene')
Function names are similar to their their BEDtools counterparts, with some additions.
- Create new interval sets with
tbl_interval()
andtbl_genome()
. Coerce existingGenomicRanges::GRanges
objects withas.tbl_interval()
.
-
Read BED and related files with
read_bed()
,read_bed12()
,read_bedgraph()
,read_narrowpeak()
andread_broadpeak()
. -
Read genome files containing chromosome name and size information with
read_genome()
. -
Load VCF files with
read_vcf()
. -
Access remote databases with
db_ucsc()
anddb_ensembl()
.
-
Adjust interval coordinates with
bed_slop()
andbed_shift()
, and create new flanking intervals withbed_flank()
. -
Combine nearby intervals with
bed_merge()
and identify nearby intervals withbed_cluster()
. -
Generate intervals not covered by a query with
bed_complement()
. -
Order intervals with
bed_sort()
.
-
Find overlaps between sets of intervals with
bed_intersect()
. -
Apply functions to overlapping sets of intervals with
bed_map()
. -
Remove intervals based on overlaps with
bed_subtract()
. -
Find overlapping intervals within a window with
bed_window()
. -
Find closest intervals independent of overlaps with
bed_closest()
.
-
Generate random intervals with
bed_random()
. -
Shuffle the coordinates of intervals with
bed_shuffle()
. -
Sample input intervals with
dplyr::sample_n()
anddplyr::sample_frac()
.
-
Calculate significance of overlaps between sets of intervals with
bed_fisher()
andbed_projection()
. -
Quantify relative and absolute distances between sets of intervals with
bed_reldist()
andbed_absdist()
. -
Quantify extent of overlap between sets of intervals with
bed_jaccard()
.
-
Create features from BED12 files with
create_introns()
,create_tss()
,create_utrs5()
, andcreate_utrs3()
. -
Visualize the actions of valr functions with
bed_glyph()
. -
Constrain intervals to a genome reference with
bound_intervals()
. -
Subdivide intervals with
bed_makewindows()
. -
Convert BED12 to BED6 format with
bed12_to_exons()
. -
Calculate spacing between intervals with
interval_spacing()
.
-
The Python library pybedtools wraps BEDtools.
-
The R packages GenomicRanges, bedr, IRanges and GenometriCorr provide similar capability with a different philosophy.