gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites

Metabolomes comprise constitutive and non-constitutive metabolites produced due to physiological, genetic or environmental effects. However, finding constitutive metabolites and non-constitutive metabolites in large datasets is technically challenging. We developed gcProfileMakeR, an R package using...

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Bibliographic Details
Published in:Metabolites 2021-03, Vol.11 (4), p.211
Main Authors: Perez-Sanz, Fernando, Ruiz-Hernández, Victoria, Terry, Marta I, Arce-Gallego, Sara, Weiss, Julia, Navarro, Pedro J, Egea-Cortines, Marcos
Format: Article
Language:English
Subjects:
automatic classification
Circadian rhythms
Clock gene
constitutive metabolome
Contaminants
Data processing
Datasets
Environmental effects
floral organ identity
gcProfileMakeR
Genotypes
Libraries
machine learning
Metabolites
non-constitutive metabolome
Retention
RNA-mediated interference
Software packages
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Summary:Metabolomes comprise constitutive and non-constitutive metabolites produced due to physiological, genetic or environmental effects. However, finding constitutive metabolites and non-constitutive metabolites in large datasets is technically challenging. We developed gcProfileMakeR, an R package using standard Excel output files from an Agilent Chemstation GC-MS for automatic data analysis using CAS numbers. gcProfileMakeR has two filters for data preprocessing removing contaminants and low-quality peaks. The first function NormalizeWithinFiles, samples assigning retention times to CAS. The second function NormalizeBetweenFiles, reaches a consensus between files where compounds in close retention times are grouped together. The third function getGroups, establishes what is considered as Constitutive Profile, Non-constitutive by Frequency i.e., not present in all samples and Non-constitutive by Quality. Results can be plotted with the plotGroup function. We used it to analyse floral scent emissions in four snapdragon genotypes. These included a wild type, and affecting floral identity and targeting a circadian clock gene. We identified differences in scent constitutive and non-constitutive profiles as well as in timing of emission. gcProfileMakeR is a very useful tool to define constitutive and non-constitutive scent profiles. It also allows to analyse genotypes and circadian datasets to identify differing metabolites.
ISSN:2218-1989
2218-1989
DOI:10.3390/metabo11040211