Construct in-house or public MS2 database for metID.

Source: R/construct_database.R

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

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 = "shenxt1990@163.com",
  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.

See also

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

Author

Xiaotao Shen shenxt1990@163.com