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 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, Deficiens nicotianoides and compacta affecting floral identity and RNAi:AmLHY 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.
Circadian clock; Constitutive metabolome; Machine learning
Perez-Sanz F, Ruiz-Hernández V, Terry MI, Arce-Gallego S, Weiss J, Navarro PJ, et al. gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites. Metabolites. 2021 Abr;11(4):211.
Use this identifier for quote and/or link this documenthttp://hdl.handle.net/11351/7642
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