Feeding BED: Dump and preprocess flat data files from Uniprot — dumpUniprotDb • BED

Not exported to avoid unintended modifications of the DB.

Usage

dumpUniprotDb(
  taxOfInt,
  divOfInt,
  release,
  ddir,
  ftp = "ftp://ftp.expasy.org/databases/uniprot",
  env = parent.frame(n = 1)
)

Arguments

taxOfInt: the organism of interest (e.g., "9606" for human, "10090" for mouse or "10116" for rat)
divOfInt: the taxonomic division to which the organism belong (e.g., "human", "rodents", "mammals", "vertebrates")
release: the release of interest (check if already downloaded)
ddir: path to the directory where the data should be saved
ftp: location of the ftp site
env: the R environment in which to load the tables when built