gcProfileMakeR

gcProfileMakeR is an R package that simplifies the identification and analysis of constitutive and non-constitutive metabolites within large datasets, a task that poses significant technical challenges. Developed to work with standard Excel output files from Agilent Chemstation GC-MS, it automates data analysis using CAS numbers, incorporating two preprocessing filters to eliminate contaminants and low-quality peaks. The package's functions include NormalizeWithinFiles, which assigns retention times to CAS for individual samples, and NormalizeBetweenFiles, which achieves consensus between files by grouping compounds with close retention times. The getGroups function categorizes metabolites into constitutive profiles, non-constitutive by frequency (not present in all samples), and non-constitutive by quality, facilitating detailed metabolomic analysis.

gcProfileMakeR's plotGroup function enables visualization of these categorizations, enhancing the interpretability of results.