Read data from bigBed files.

Read data from bigBed files.

Usage

read_bigbed(bbfile, chrom = NULL, start = NULL, end = NULL, convert = TRUE)

Arguments

bbfile

filename for bigBed file

chrom

read data for specific chromosome

start

start position for data

end

end position for data

convert

convert bigBed values to individual columns

Value

tibble

See also

https://github.com/dpryan79/libBigWig

https://github.com/brentp/bw-python

Examples

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> <chr> <chr>  <chr>      <chr>    <chr>    <chr>     
#> 1 chr1  4.80e6 4.80e6 test… 1     +      4797973    4836816  1        9         
#> 2 chr10 4.85e6 4.85e6 diff… 1     +      4848118    4880877  1        6         
#> 3 chr20 5.07e6 5.07e6 negs… 1     -      5073253    5152630  1        14        
#> # ℹ 2 more variables: blockSizes <chr>, chromStarts <chr>

read_bigbed(bb, chrom = "chr10")
#> # A tibble: 1 × 12
#>   chrom  start    end name  score strand thickStart thickEnd reserved blockCount
#>   <chr>  <int>  <int> <chr> <chr> <chr>  <chr>      <chr>    <chr>    <chr>     
#> 1 chr10 4.85e6 4.85e6 diff… 1     +      4848118    4880877  1        6         
#> # ℹ 2 more variables: blockSizes <chr>, chromStarts <chr>