E5S_metabolomics_workflow.R

Easy 5 Steps metabolomics workflow

E5S metabolomics workflow.R was used for fully processing peak table in .csv format. All .csv files were placed in a working directory, each first column - sample name, second - "Label", other - numeric values or NA. Row and column names should be presented.

ds_raw.csv is data table of own dataset after integration and HM MVI.

To simplify the calculations, name the data tables according to:

• raw data (ds_raw.csv)
• ds_raw after EigenMS (dsr.csv)
• dsr after UVF+MVI (ds.csv)
• ds after ML+SFE (ds_d.csv)
• ds_d after RFE (ds_rfe.csv)
• raw data after UVF+MVI (ds_raw_ds.csv)

Citation:

Plyushchenko Ivan, et al. "An approach for feature selection with data modelling in LC-MS metabolomics." Analytical Methods 12.28 (2020): 3582-3591.

Dataset Ref:

Metabolomics Workbench project PR000857, study ST001271

Contact:

Please send any comment, suggestion or question you may have to the author (Dr. Ivan Plyushchenko), email: plyushchenko.ivan@gmail.com.