buildExtDB: Build external database using a given base database

In MetaDBparse: Annotate Mass over Charge Values with Databases and Formula Prediction

Description

Wrapper function that takes a base database, an existing (or not) external database, and fills the extended database with adduct and isotope variants of the compounds in the base database.

Usage

buildExtDB(
  outfolder,
  ext.dbname = "extended",
  base.dbname,
  cl = 0,
  blocksize = 600,
  mzrange = c(60, 600),
  adduct_table = adducts,
  adduct_rules = adduct_rules,
  silent = silent,
  use.rules = TRUE,
  count.isos = F,
  all.isos = T
)

Arguments

outfolder	Which folder are your databases in?
ext.dbname	Extended database name (without .db suffix), Default: 'extended'
base.dbname	Base database name (without .db suffix)
cl	parallel::makeCluster object for multithreading, Default: 0
blocksize	How many compounds to process simultanaously? Higher means more memory spikes but faster building, Default: 600
mzrange	Range of m/zs to include in database, Default: c(60, 600)
adduct_table	Adduct table, Default: adducts
adduct_rules	Adduct rule table, Default: adduct_rules
silent	Silence warnings?, Default: silent
use.rules	Use adduct rules?, Default: TRUE
count.isos	Add columns for amounts of 2H, 13C, 15N atoms? Useful for heavy isotope experiments.
all.isos	Include and calculate all isotopes? (if FALSE, only takes the 100/main isotope).

See Also

SQLite fn as.data.table,rbindlist,fwrite,fread dbWriteTable pbapply check_chemform

Examples

 ## Not run: myFolder = tempdir()
 ## Not run: buildBaseDB(outfolder = myFolder, "lmdb", test = TRUE)
 ## Not run: file.remove(file.path(myFolder, "extended.db"))
 ## Not run: data(adducts)
 ## Not run: data(adduct_rules)
 ## Not run: buildExtDB(outfolder = myFolder, base.dbname = "lmdb",
 silent=FALSE, adduct_table = adducts, adduct_rules = adduct_rules)
## End(Not run)

MetaDBparse documentation built on May 3, 2021, 5:09 p.m.