| Type: | Package |
| Title: | Read bigWig and bigBed Files |
| Version: | 0.1.1 |
| Description: | Read bigWig and bigBed files using "libBigWig" https://github.com/dpryan79/libBigWig. Provides lightweight access to the binary bigWig and bigBed formats developed by the UCSC Genome Browser group. |
| License: | MIT + file LICENSE |
| URL: | https://rnabioco.github.io/cpp11bigwig/, https://github.com/rnabioco/cpp11bigwig |
| BugReports: | https://github.com/rnabioco/cpp11bigwig/issues |
| Imports: | GenomicRanges, IRanges, tibble |
| Suggests: | testthat (≥ 3.0.0) |
| LinkingTo: | cpp11 |
| Config/Needs/website: | rnabioco/rbitemplate |
| Config/testthat/edition: | 3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| NeedsCompilation: | yes |
| Packaged: | 2025-01-19 21:46:21 UTC; jayhesselberth |
| Author: | Jay Hesselberth [aut, cre], RNA Bioscience Initiative [fnd, cph], Devon Ryan [cph] |
| Maintainer: | Jay Hesselberth <jay.hesselberth@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2025-01-19 22:10:11 UTC |
cpp11bigwig: read data from bigWig files
Description
bigwig provides methods to read data from bigWig files. bigwig uses cpp11 to wrap libBigWig from @dpryan79.
Details
https://github.com/dpryan79/libBigWig
Author(s)
Jay Hesselberth jay.hesselberth@gmail.com
See Also
Useful links:
Report bugs at https://github.com/rnabioco/cpp11bigwig/issues
Read data from bigBed files.
Description
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)
read_bigbed(bb, chrom = "chr10")
Read data from bigWig files.
Description
Read data from bigWig files.
Usage
read_bigwig(bwfile, chrom = NULL, start = NULL, end = NULL, as = NULL)
Arguments
bwfile |
filename for bigWig file |
chrom |
read data for specific chromosome |
start |
start position for data |
end |
end position for data |
as |
return data as a specific type.
The default is a tibble ( |
Value
tibble
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")