dumpNcbiDb {BED}

Feeding BED: Dump tables from the NCBI gene DATA

Description

Not exported to avoid unintended modifications of the DB.

Usage

dumpNcbiDb(
  taxOfInt,
  reDumpThr,
  ddir,
  toLoad = c("gene_info", "gene2ensembl", "gene_group", "gene_orthologs", "gene_history",
    "gene2refseq"),
  env = parent.frame(n = 1),
  curDate
)

Arguments

taxOfInt

the organism to download (e.g. "9606").

reDumpThr

time difference threshold between 2 downloads

ddir

path to the directory where the data should be saved

toLoad

the list of tables to load

env

the R environment in which to load the tables when downloaded

curDate

current date as given by Sys.Date