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This function will output a 4 column tibble with zero-based chrom, start, end, value columns.

Usage

read_bigwig(path, ...)

Arguments

path

path to bigWig file

...

params for cpp11bigwig::read_bigwig()

Examples

read_bigwig(valr_example("hg19.dnase1.bw"))
#> # A tibble: 2,587 × 4
#>    chrom    start      end value
#>    <chr>    <int>    <int> <dbl>
#>  1 chr22 16050284 16050464     1
#>  2 chr22 16051024 16051204     1
#>  3 chr22 16051224 16051764     1
#>  4 chr22 16052724 16052904     1
#>  5 chr22 16053224 16053404     1
#>  6 chr22 16054584 16054644     1
#>  7 chr22 16054644 16054764     2
#>  8 chr22 16054764 16054824     1
#>  9 chr22 16056404 16056424     1
#> 10 chr22 16056424 16056584     2
#> # ℹ 2,577 more rows

read_bigwig(valr_example("hg19.dnase1.bw"), as = "GRanges")
#> GRanges object with 2587 ranges and 1 metadata column:
#>          seqnames            ranges strand |     score
#>             <Rle>         <IRanges>  <Rle> | <numeric>
#>      [1]    chr22 16050284-16050464      * |         1
#>      [2]    chr22 16051024-16051204      * |         1
#>      [3]    chr22 16051224-16051764      * |         1
#>      [4]    chr22 16052724-16052904      * |         1
#>      [5]    chr22 16053224-16053404      * |         1
#>      ...      ...               ...    ... .       ...
#>   [2583]    chr22 17145624-17145804      * |         1
#>   [2584]    chr22 17148024-17148064      * |         1
#>   [2585]    chr22 17148064-17148124      * |         2
#>   [2586]    chr22 17148124-17148144      * |         3
#>   [2587]    chr22 17148144-17148204      * |         5
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths