Metabolomics data processing for the ADNI data sets. Currently, only supports the Biocrates p180 and Nightingale NMR platforms.
metabo_adni is distributed as a python package, so install it by running:
pip install metabo_adniIn the folder with the required datasets, simply run:
clean_filesAnd metabo_adni will run with the default parameters. Note: do not change the original name of the files.
-D: define the directory were the files are located. Default, current working directory-P: define the platform, either p180 or nmr. Default, p180-F: define the fasting file. Default, BIOMARK.csv-L: define the directory were the LOD p180 files are located. Default, current working directory--mmc: remove metabolites with missing proportions greater than cutoff. Default, 0.2--mpc: remove participants with missing proportions greater than cutoff. Default, 0.2--cv: remove metabolites with CV values greater than cutoff. Default, 0.2--icc: remove metabolites with ICC values lower than cutoff. Default, 0.65--log2: apply log2 transformation to metabolite concentration values--merge: merge data frames across cohorts--zscore: apply zscore transformation to metabolite concentration values--winsorize: winsorize extreme values (more than 3 std of mean)--remove-moutliers: remove multivariate outliers using the Mahalanobis distance--residualize-meds: replace metabolite values with residuals from a regression with medication intake. Note that residuals are scaled to unit variance