Lilikoi: An R Package For Personalized Pathway-Based Classification Modeling Using Metabolomics Data
GIGASCIENCE(2018)
Abstract
Lilikoi (the Hawaiian word for passion fruit) is a new and comprehensive R package for personalized pathway-based classification modeling using metabolomics data. Four basic modules are presented as the backbone of the package: feature mapping module, which standardizes the metabolite names provided by users and maps them to pathways; dimension transformation module, which transforms the metabolomic profiles to personalized pathway-based profiles using pathway deregulation scores; feature selection module, which helps to select the significant pathway features related to the disease phenotypes; and classification and prediction module, which offers various machine learning classification algorithms.
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Key words
metabolomics,pathway,classification,feature selection,machine learning,mapping
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