Pull subset DB

Pull a subset database from a given "archive" database based on a given start date and end date and a variant file

pull_subset_db(
  archiveFile,
  startDate,
  endDate,
  NewDBFile,
  variantFile,
  force = FALSE,
  silently = TRUE
)

Arguments

archiveFile

string name of archive db file or db file to subset from, e.g. "databases/All_Assay_Archive.db"

startDate

string start date of data to be included in subset db, e.g. "2022-05"

endDate

string end date of data to be included in subset db, e.g. "2022-07"

NewDBFile

string name of new subset db file, e.g. "DB_files/DB_3M/all_May-July_SD08-15_subgroups.db"

variantFile

string name of .csv file containing breakdown of lineage/subgroup names of sequences, e.g. "who_lineages_subgroups.csv"

force

logical value indicating whether or not to force override already existing subset db with same name

silently

logical value indicating whether to print tables created in subset db