gcProfileMakeR: An R package for automatic classification of constitutive and non-constitutive metabolites
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Pérez Sanz, Fernando; Ruiz Hernández, María Victoria; Terry López, Marta Isabel; Arce Gallego, Sara; Weiss, Julia Rosl; [et al.]Área de conocimiento
Lenguajes y Sistemas InformáticosPatrocinadores
This research was funded by Ministerio de Ciencia, Innovación y Universidades and FEDER grant numbers BFU2017-88300-C2-1R to M.E.-C. and J.W.; BFU2017-88300-C2-2R to P.J.N.; and a PhD contract by the Ministerio de Educación Cultura y Deporte FPU13/03606 to V.R.-H.Fecha de publicación
2021-03Editorial
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Perez-Sanz, F.; Ruiz-Hernández, V.; Terry, M.I.; Arce-Gallego, S.; Weiss, J.; Navarro, P.J.; Egea-Cortines, M. gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites. Metabolites 2021, 11, 211. https://doi.org/10.3390/metabo11040211Revisión por pares
siPalabras clave
automatic classificationgcProfileMakeR
constitutive metabolome
non-constitutive metabolome
machine learning
floral organ identity
R package
circadian clock
Resumen
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 ...
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