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Genome Interval Arithmetic in R
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valr provides tools to read and manipulate genome intervals and signals,similar to theBEDtoolssuite.
# Install released version from CRANinstall.packages("valr")
# Install development version from GitHub# install.packages("pak")pak::pak("rnabioco/valr")
Functions in valr have similar names to their BEDtools counterparts, andso will be familiar to users coming from the BEDtools suite. Unlikeother tools that wrap BEDtools and write temporary files to disk, valrtools run natively in memory. Similar topybedtools, valrhas 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 regionsintergenic<- bed_subtract(snps,genes)# find distance from intergenic snps to nearest genenearby<- 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#> <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#> # ℹ 1,037 more rows
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