GitHub - rnabioco/valr: Genome Interval Arithmetic in R (original) (raw)

valr

valr provides tools to read and manipulate genome intervals and signals, similar to the BEDtoolssuite.

Installation

Install released version from CRAN

install.packages("valr")

Install development version from GitHub

install.packages("pak")

pak::pak("rnabioco/valr")

valr Example

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 topybedtools, valr has a terse syntax:

library(valr) library(dplyr)

snps <- read_bed(valr_example("hg19.snps147.chr22.bed.gz")) genes <- read_bed(valr_example("genes.hg19.chr22.bed.gz"))

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 × 4 #> name.x name.y .overlap .dist #> #> 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 #> # ℹ 1,037 more rows