rc.cmpd.get.classyfire: getClassyFire

In RAMClustR: Mass Spectrometry Metabolomics Feature Clustering and Interpretation

getClassyFire

Description

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

Usage

rc.cmpd.get.classyfire(
  ramclustObj = NULL,
  inchikey = NULL,
  get.all = TRUE,
  max.wait = 10,
  posts.per.minute = 5
)

Arguments

ramclustObj	ramclustR object to ClassyFy. Must supply one of either ramclustObj or inchikey (see below)
inchikey	vector of text inchikeys to ClassyFy. Must supply one of either ramclustObj or inchikey.
get.all	logical; if TRUE, when inchikey classyfire lookup fails, submits for classyfication. Can be slow. max.wait (below) sets max time to spend on each compound before moving on. default = FALSE.
max.wait	numeric; maximum time (seconds) to wait per compound when 'get.all' = TRUE.
posts.per.minute	integer; a limit set when 'get.all' is true. ClassyFire server accepts no more than 5 posts per minute when calculating new ClassyFire results. Slows down submission process to keep server from denying access.

Details

The $inchikey slot is used to look up the

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

RAMClustR documentation built on Oct. 20, 2023, 5:08 p.m.