get.classyfire.local: get.classyfire.local

In cbroeckl/csu.pmf.tools: a collection of features used internally at CSU PMF for non-targeted metabolomics data processing

get.classyfire.local

Description

use classyfire web API to look up full ClassyFire hirarchy for each inchikey

Usage

get.classyfire.local(
  ramclustObj = NULL,
  chemontid = NULL,
  chemont.obo.location = NULL
)

Arguments

ramclustObj	ramclustR object to ClassyFy. Must supply one of either ramclustObj or inchikey (see below)
chemontid	vector of chem ontology IDs.
chemont.obo.location	location of the chemontology OBO file.

Details

The get chem ontology heirarchy from chemontid. references local .obo file for faster lookup

Value

returns a ramclustR object. new dataframe in $classyfire slot with rows equal to number of compounds.

Author(s)

Corey Broeckling

References

Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61. DOI: 10.1186/s13321-016-0174-y

cbroeckl/csu.pmf.tools documentation built on Jan. 26, 2024, 6:27 p.m.