buildBaseDB: Build the base database

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

Description

This is a large wrapper function that calls upon all individual database parsers, cleans the resulting database and saves it in a SQLite database.

Usage

buildBaseDB(
  outfolder,
  dbname,
  custom_csv_path = NULL,
  smitype = "Canonical",
  silent = TRUE,
  cl = 0,
  test = FALSE,
  doBT = FALSE,
  btOpts = "phaseII:1",
  btLoc,
  skipClean = F
)

Arguments

outfolder	In which folder are you building your databases? Temp folders etc. will be put here.
dbname	Which database do you want to build? Options: chebi,maconda,kegg,bloodexposome,dimedb,expoexplorer, foodb, drugbank, lipidmaps, massbank, metabolights, metacyc, phenolexplorer, respect, wikidata, wikipathways, t3db, vmh, hmdb, smpdb, lmdb, ymdb, ecmdb, bmdb, rmdb, stoff, anpdb, mcdb, mvoc, pamdb
custom_csv_path	PARAM_DESCRIPTION, Default: NULL
smitype	Which SMILES format do you want?, Default: 'Canonical'
silent	Suppress warnings?, Default: TRUE
cl	parallel::makeCluster object for multithreading, Default: 0
test	Run in test mode? Makes an incomplete ver of db, but is faster.
doBT	Do a biotransformation step using Biotransformer?
btOpts	Biotransfomer -q options. Defaults to phase II transformation only.
btLoc	Location of Biotransformer JAR file. Needs to be executable!
skipClean	Skip cleaning step? Cleaning step uses SMILES to acquire formula, charge, and transforms SMILES into 'smitype' dialect.

Value

Nothing, writes SQLite database to 'outfolder'.

See Also

fread,as.data.table dbDisconnect

Examples

 ## Not run: buildBaseDB(outfolder = tempdir(), "lmdb", test=TRUE)

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