Fig. 4

Data and code availability in the ProMetIS package²⁷. The data are available in the extdata folder, which is organized into subfolders corresponding to the successive steps of the analysis (e.g., 1_processed, 2_post_processed, 5_aggregated, etc.). Within each subfolder, the 9 datasets are stored as a triplet of tabular files containing the matrix of intensities (dataMatrix.tsv), the sample metadata (sampleMetadata.tsv) and the variable metadata (variableMetadata.tsv). For each step, a vignette describes the methods used to process the data. As an example, the 2_post_processed vignette details how the datasets were post-processed, between the 1_processed and the 2_post_processed folders (note that only the post-processing of the metabolomics files is described, since the proteomics files were post-processed separately with the ProStaR software). The package thus provides a full access to both data and code, to ensure reproducibility of the results. The tutorial vignette describes how to access the final aggregated data to perform integrative bioinformatics and biostatistics analyses.