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Read a bed file into a data frame

Source: R/genomeAnnotations.R
read_bed.Rd

Bed files can contain peak or blacklist annotations. These utilities help read thos annotations

Usage

read_bed(
  path,
  additional_columns = character(0),
  backup_url = NULL,
  timeout = 300
)

read_encode_blacklist(
  dir,
  genome = c("hg38", "mm10", "hg19", "dm6", "dm3", "ce11", "ce10"),
  timeout = 300
)

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

Value

Data frame with coordinates using the 0-based convention.

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

See also

read_gtf(), read_gencode_genes()