Bed files can contain peak or blacklist annotations. These utilities help read thos annotations
Arguments
- path
Path to file (or desired save location if backup_url is used)
- additional_columns
Names for additional columns in the bed file
- backup_url
If path does not exist, provides a URL to download the gtf from
- timeout
Maximum time in seconds to wait for download from backup_url
- dir
Output directory to cache the downloaded gtf file
- genome
genome name
Details
read_bed
Read a bed file from disk or a url.
read_encode_blacklist
Downloads the Boyle Lab blacklist, as described in https://doi.org/10.1038/s41598-019-45839-z
Examples
## Dummy bed file creation
data.frame(
chrom = rep("chr1", 6),
start = seq(20, 121, 20),
end = seq(39, 140, 20)
) %>% write.table("./references/example.bed", row.names = FALSE, col.names = FALSE, sep = "\t")
#> Warning: cannot open file './references/example.bed': No such file or directory
#> Error in file(file, ifelse(append, "a", "w")): cannot open the connection
#######################################################################
## read_bed() example
#######################################################################
read_bed("./references/example.bed")
#> Error: In function read_bed: "path" is not a valid file path (file not found)
#> ▆
#> 1. └─pkgdown::build_reference("r", lazy = FALSE)
#> 2. ├─pkgdown:::unwrap_purrr_error(...)
#> 3. │ └─base::withCallingHandlers(...)
#> 4. └─purrr::map(...)
#> 5. └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
#> 6. ├─purrr:::with_indexed_errors(...)
#> 7. │ └─base::withCallingHandlers(...)
#> 8. ├─purrr:::call_with_cleanup(...)
#> 9. └─pkgdown (local) .f(.x[[i]], ...)
#> 10. ├─base::withCallingHandlers(...)
#> 11. └─pkgdown:::data_reference_topic(...)
#> 12. └─pkgdown:::run_examples(...)
#> 13. └─pkgdown:::highlight_examples(code, topic, env = env)
#> 14. └─downlit::evaluate_and_highlight(...)
#> 15. └─evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler)
#> 16. └─evaluate:::evaluate_call(...)
#> 17. ├─evaluate (local) timing_fn(...)
#> 18. ├─evaluate (local) handle(...)
#> 19. │ └─base::try(f, silent = TRUE)
#> 20. │ └─base::tryCatch(...)
#> 21. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#> 22. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#> 23. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
#> 24. ├─base::withCallingHandlers(...)
#> 25. ├─base::withVisible(...)
#> 26. └─evaluate:::eval_with_user_handlers(expr, envir, enclos, user_handlers)
#> 27. └─base::eval(expr, envir, enclos)
#> 28. └─base::eval(expr, envir, enclos)
#> 29. └─BPCells::read_bed("./references/example.bed")
#> 30. └─BPCells:::assert_is_file(...) at r/R/genomeAnnotations.R:231:3
#######################################################################
## read_encode_blacklist() example
#######################################################################
read_encode_blacklist("./reference")
#> # A tibble: 636 × 4
#> chr start end reason
#> <chr> <dbl> <dbl> <chr>
#> 1 chr10 0 45700 Low Mappability
#> 2 chr10 38481300 38596500 High Signal Region
#> 3 chr10 38782600 38967900 High Signal Region
#> 4 chr10 39901300 41712900 High Signal Region
#> 5 chr10 41838900 42107300 High Signal Region
#> 6 chr10 42279400 42322500 High Signal Region
#> 7 chr10 126946300 126953400 Low Mappability
#> 8 chr10 133625800 133797400 High Signal Region
#> 9 chr11 0 194500 Low Mappability
#> 10 chr11 518900 520700 Low Mappability
#> # ℹ 626 more rows
