export.ComboundDb: export.ComboundDb

Description

export pubchem.bio pc.bio syle data.table to a CompoundDb database

Usage

export.ComboundDb(
  pc.bio.object = NULL,
  pc.directory = NULL,
  path = NULL,
  dbFile = NULL,
  source = NULL,
  source_version = NULL,
  url = NULL,
  source_date = NULL,
  organism = NA_character_,
  get.synonyms = FALSE
)

Value

'CompDb' from CompoundDb package. see vignette('create-compounddb', package = 'CompoundDb')

Arguments

pc.bio.object: input data.table, generated from 'build.pubchem.bio' or 'build.taxon.metabolome' functions
pc.directory: directory from which to load pubchem .Rdata files. alternatively, provide R data.tables for ALL cid.property.object options defined below.
path: valid file path specifying the directory to which the database will be saved.
dbFile: valid file name - use .sqlite extension. if NULL, will set to 'pubchem.bio.sqlite'
source: default = NULL. if NULL, will set to 'pubchem.bio'
source_version: default = NULL. if NULL, will set to pubchem.bio version.
url: default = NULL. if NULL, will set to "https://cran.r-project.org/web/packages/pubchem.bio/index.html"
source_date: default = NULL. if NULL, will set to current date via format(Sys.Date(), format = "%Y-%m-%d")
organism: character. default = NA_character_. if this is a species specific database, set to species name or NCBI taxonomy ID number.
get.synonyms: logical. default = FALSE. When TRUE, will load the 'cid.synonyms.Rdata' file from the pc.directory, which must be defined. database product will have all synonyms included. If FALSE, synonyms will be an empty list.

Author

Corey Broeckling

Details

takes output from 'build.pubchem.bio' or 'build.taxon.metabolome' functions, reformatting, and converting to a CompoundDb object and database. see see vignette('create-compounddb', package = 'CompoundDb') for more details on the CompoundDb package