Package 'cpp11bigwig'

Read data from bigBed files.

Description

Columns are automatically typed based on the autoSql schema embedded in the bigBed file. Integer types (uint, int) become R integers, floating point types (float, double) become R doubles, and all other types (including array types like int[blockCount]) remain as character strings.

Usage

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

Arguments

bbfile	path or URL for a bigBed file. Remote files (⁠http://⁠, ⁠https://⁠, ⁠ftp://⁠) are supported when the package was installed with libcurl available.
chrom	read data for specific chromosome
start	start position for data
end	end position for data

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)

read_bigbed(bb, chrom = "chr10")

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Read data from bigWig files.

Description

Read data from bigWig files.

Usage

read_bigwig(
  bwfile,
  chrom = NULL,
  start = NULL,
  end = NULL,
  as = NULL,
  fill = 0
)

Arguments

bwfile	path or URL for a bigWig file. Remote files (⁠http://⁠, ⁠https://⁠, ⁠ftp://⁠) are supported when the package was installed with libcurl available.
chrom	read data for specific chromosome
start	start position for data
end	end position for data
as	return data as a specific type. One of "tbl" (the default tibble), "GRanges", or "Rle". "Rle" returns a per-base run-length-encoded vector spanning the requested range (see Details).
fill	value used for bases with no data when as = "Rle". Defaults to 0 (the convention for coverage); use NA to mark uncovered bases as missing. Ignored for other as values.

Details

When as = "Rle", the result is an S4Vectors::Rle whose expanded length equals the queried range, i.e. end - start when both are supplied, otherwise the extent of the returned data for each chromosome. Bases with no data in the file are set to fill. bigWig coordinates are 0-based and half-open, so element i corresponds to genomic position start + i - 1. A single-chromosome query returns a bare Rle; a multi-chromosome query returns a named IRanges::RleList.

Value

A tibble, GRanges, or Rle/RleList depending on as.

See Also

https://github.com/dpryan79/libBigWig

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

Examples

bw <- system.file("extdata", "test.bw", package = "cpp11bigwig")

read_bigwig(bw)

read_bigwig(bw, chrom = "10")

read_bigwig(bw, chrom = "1", start = 100, end = 130)

read_bigwig(bw, as = "GRanges")

read_bigwig(bw, chrom = "1", start = 100, end = 130, as = "Rle")

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