cpp11bigwig provides read-only access to bigWig and bigBed files using libBigWig https://github.com/dpryan79/libBigWig.
# Install released version from CRAN
install.packages("cpp11bigwig")# Install development version from GitHub
# install.packages("pak")
pak::pak("rnabioco/cpp11bigwig")library(cpp11bigwig)
bw <- system.file("extdata", "test.bw", package = "cpp11bigwig")
read_bigwig(bw)
#> # A tibble: 6 × 4
#> chrom start end value
#> <chr> <int> <int> <dbl>
#> 1 1 0 1 0.100
#> 2 1 1 2 0.200
#> 3 1 2 3 0.300
#> 4 1 100 150 1.40
#> 5 1 150 151 1.5
#> 6 10 200 300 2
bb <- system.file("extdata", "test.bb", package = "cpp11bigwig")
read_bigbed(bb)
#> # A tibble: 3 × 12
#> chrom start end name score strand thickStart thickEnd reserved blockCount
#> <chr> <int> <int> <chr> <int> <chr> <int> <int> <int> <int>
#> 1 chr1 4.80e6 4.84e6 test… 1 + 4797973 4836816 1 9
#> 2 chr10 4.85e6 4.88e6 diff… 1 + 4848118 4880877 1 6
#> 3 chr20 5.07e6 5.15e6 negs… 1 - 5073253 5152630 1 14
#> # ℹ 2 more variables: blockSizes <chr>, chromStarts <chr>