prepareCompoundList: Preparation of compound list

In michaelwitting/masstrixR: Annotation of MS based metabolomics data

Description

A compound list that can be used with masstrixR can be generated on the fly. Minimum input is a data frame with the following columns: metabolite id ($id), SMILES ($smiles), InChI ($inchi), InChIKey ($inchikey), formula ($formula) metabolite name ($name) and an exact mass ($exactmass). Furthermore, the adducts that shall be covered in the DB have to be defined. This can be either done by using an list of adducts or supplying a adduct definition for each metabolite with an additiona adduct column ($adducts). If it is intended to perform retetion time and collisional cross section matching columns containing this information are required ($rt and $ccs). In case of CCS matching, individual adduct rules are required since each adduct has a different CCS value. Examples for each input are found in the examples in the vignettes.

Usage

prepareCompoundList(compoundList, adductList = NA, rt = FALSE,
  ccs = FALSE, extId = FALSE)

Arguments

compoundList	List of compounds that shall be added to DB
adductList	Vector with adducts that shall be covered in the DB.
rt	Boolean value indicating if compound list contains RT data
ccs	Boolean value indicating if compound list contains CCS data

Value

Returns a data frame suitable for upload to a SQLite DB.

Author(s)

Michael Witting, [e-mail]

See Also

validateCompoundList

createDb

Examples

prepareCompoundList(compoundList, adducts = c("M+H", "M+Na"))

michaelwitting/masstrixR documentation built on Nov. 8, 2019, 8:12 p.m.