construct_database: Construct in-house or public MS2 database for metID.

In jaspershen/metID: Metabolite identification based on MS1 and MS2 spectra

Construct in-house or public MS2 database for metID.

Description

Construct MS2 spectra database according to mzXML data and compound information table (csv format).

Usage

construct_database(
  path = ".",
  version = "0.0.1",
  metabolite.info.name = "metabolite.info.csv",
  source = "Michael Snyder Lab",
  link = "http://snyderlab.stanford.edu/",
  creater = "Xiaotao Shen",
  email = "[e-mail]",
  rt = TRUE,
  mz.tol = 15,
  rt.tol = 30,
  threads = 3
)

Arguments

path	Work directory.
version	The version of you database. Default is 0.0.1.
metabolite.info.name	The metabolite information table name, it must be csv format. The demo data can be got from the 'demoData' package. Please see https://jaspershen.github.io/metID/articles/metID.html
source	The source of your database.
link	Website link of the source.
creater	Creater name. For example, Xiaotao Shen.
email	email address.
rt	Do the metabolites have RT information or not?. If not, set it as FALSE.
mz.tol	m/z tolerance for the match between metabolites and precursor m/z of MS2 spectra.
rt.tol	RT tolerance for the match between metabolites and precursor m/z of MS2 spectra.
threads	The number of threads

Value

A databaseClass object.

Author(s)

Xiaotao Shen [e-mail]

See Also

The example and demo data of this function can be found https://jaspershen.github.io/metID/articles/metID.html

jaspershen/metID documentation built on July 31, 2022, 11:31 p.m.