FastRet (version 1.3.0)

read_retip_hilic_data: Read the HILIC dataset from the Retip package

Description

Reads the Retip::HILIC dataset (CC BY 4.0) from the Retip package or, if Retip is not installed, downloads the dataset directly from the Retip GitHub repository. Before returning the dataset, SMILES strings are canonicalized and the original tibble object is converted to a base R data.frame.

Usage

read_retip_hilic_data(verbose = 1)

Value

A data frame with 970 rows and the following columns:

• NAME: Molecule name

• INCHIKEY: InChIKey

• SMILES: Canonical SMILES string

• RT: Retention time in Minutes

Arguments

verbose

Verbosity. 1 for messages, 0 to suppress them.

Details

Attribution as required by CC BY 4.0:

• Original dataset by: Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn as part of the Retip project.
  

• Source repository: https://github.com/oloBion/Retip
  

• Original file: https://github.com/oloBion/Retip/raw/master/data/HILIC.RData
  

• License: CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/)
  

• Modifications in FastRet:

  • converted tibble to data.frame

  • canonicalized SMILES using as_canonical()

  • renamed column 'INCHKEY' to 'INCHIKEY'

References

Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics
Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn
Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765

Examples

df <- read_retip_hilic_data(verbose = 0)