chemodiv (version 0.3.1)

NPCTable: Generate NPClassifier classification

Description

Function to classify compounds with NPClassifier, and put the results in a data frame containing the pathway, superclass and class for each compound.

Usage

NPCTable(compoundData)

Value

Data frame with the NPClassifier classification for each compound as pathway, superclass and class. Note that compounds may be classified in more than one group, or no group, at each level of classification.

Arguments

compoundData

Data frame with the chemical compounds of interest, usually the compounds found in the sample dataset. Should include a column named "compound" with common names of the compounds and a column named "smiles" with SMILES IDs of the compounds.

Details

NPClassifier (Kim et al. 2021) is a deep-learning tool that automatically classifies natural products (i.e. phytochemical compounds) into a hierarchical classification of three levels: pathway, superclass and class. This classification largely corresponds to the biosynthetic groups/pathways the compounds are produced in. The NPCTable function conveniently performs this classification directly in R on the compounds in compoundData, by accessing the tool at https://npclassifier.gnps2.org/ and downloading the classifications.

References

Kim HW, Wang M, Leber CA, Nothias L-F, Reher R, Kang KB, van der Hooft JJJ, Dorrestein PC, Gerwick WH, Cottrell GW. 2021. NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products. Journal of Natural Products 84: 2795-2807.

Examples

data(minimalCompData)
NPCTable(minimalCompData)

data(alpinaCompData)
NPCTable(compoundData = alpinaCompData[1:3,]) # First three compounds only