fooddb2msfinder: foodb2msfinder

View source: R/fooddb2msfinder.R

fooddb2msfinderR Documentation

foodb2msfinder

Description

convenience function for converting FoodDB database export format to MSFinder custom database import format. Before running this, please have downloaded .csv files from FoodDB with the appropriate Display Field Headers (see details)

Usage

fooddb2msfinder(
  foodb.files = NULL,
  out.dir = NULL,
  out.name = "FoodDB_for_MSFinder.txt"
)

Arguments

foodb.files

default = NULL, if path is set, will read automatically. If NULL, direcory selection by user.

out.dir

default = NULL. Can set to exiseting directory with full path name. If NULL, direcory selection by user.

out.name

default = "FoodDB_for_MSFinder.txt".

Details

Input file(s) should be csv formatted, with required headers of 'Name', 'Smiles', 'Inchikey', 'Chemical formula', and 'Mono mass' - case sensitive. Output will be in tab delimited text format in directory of choice.

Value

Nothing is returned - output file written to directory set by 'out.dir' and name set by 'out.name'

Author(s)

Corey Broeckling

References

Broeckling CD, Afsar FA, Neumann S, Ben-Hur A, Prenni JE. RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data. Anal Chem. 2014 Jul 15;86(14):6812-7. doi: 10.1021/ac501530d. Epub 2014 Jun 26. PubMed PMID: 24927477.


cbroeckl/csu.pmf.tools documentation built on May 21, 2024, 1:26 a.m.