MetaDBparse (version 2.0.0)

buildBaseDB: Build the base database

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 {
 
# }
# NOT RUN {
buildBaseDB(outfolder = tempdir(), "lmdb", test=TRUE)
# }