Download the FANTOM CAT Companion Tables

Fetches, for one FANTOM CAT level, the ID mapping table (transcript to CAGE cluster), the gene information table and the CAGE cluster BED file, which add_fantom_cat_tables() joins into an annotation directory.

Usage

download_fantom_cat_tables(
  level = c("lv3_robust", "lv4_stringent", "lv2_permissive", "lv1_raw"),
  tables = c("id_mapping", "gene_info", "cage_clusters"),
  output_path = ":cache:",
  timeout_limit = 3600,
  method = "auto"
)

Arguments

level

FANTOM CAT level: "lv3_robust" (default), "lv1_raw", "lv2_permissive" or "lv4_stringent".

tables

Which tables to download.

output_path

Directory where the file is saved. Defaults to ":cache:", the package cache (see get_isoformic_cache()).

timeout_limit

Maximum time in seconds for the download. Takes precedence over options("timeout"). Defaults to 3600.

method

Method used by utils::download.file(). Defaults to "auto".

Value

A named character vector of file paths (id_mapping, gene_info, cage_clusters).

Examples

if (FALSE) { # \dontrun{
tables <- download_fantom_cat_tables("lv3_robust")
tables
} # }