BED files use 0-based coordinate starts, while gggenomes uses 1-based start coordinates. BED file coordinates are therefore transformed into 1-based coordinates during import.

read_bed(file, col_names = def_names("bed"), col_types = def_types("bed"), ...)

Arguments

file

Either a path to a file, a connection, or literal data (either a single string or a raw vector).

Files ending in .gz, .bz2, .xz, or .zip will be automatically uncompressed. Files starting with http://, https://, ftp://, or ftps:// will be automatically downloaded. Remote gz files can also be automatically downloaded and decompressed.

Literal data is most useful for examples and tests. To be recognised as a path, it must be wrapped with I(), be a string containing at least one new line, or be a vector containing at least one string with a new line.

Using a value of clipboard() will read from the system clipboard.

col_names

column names to use. Defaults to def_names("bed") compatible with canonical bed files. def_names("bed") can easily be combined with extra columns: col_names = c(def_names("bed"), "more", "things").

col_types

One of NULL, a cols() specification, or a string. See vignette("readr") for more details.

If NULL, all column types will be imputed from the first 1000 rows on the input. This is convenient (and fast), but not robust. If the imputation fails, you'll need to increase the guess_max or supply the correct types yourself.

Column specifications created by list() or cols() must contain one column specification for each column. If you only want to read a subset of the columns, use cols_only().

Alternatively, you can use a compact string representation where each character represents one column:

  • c = character

  • i = integer

  • n = number

  • d = double

  • l = logical

  • f = factor

  • D = date

  • T = date time

  • t = time

  • ? = guess

  • _ or - = skip

    By default, reading a file without a column specification will print a message showing what readr guessed they were. To remove this message, set show_col_types = FALSE or set `options(readr.show_col_types = FALSE).

Value