Metabo_ADNI

Metabolomics data processing for the ADNI data sets. Currently, only supports the Biocrates p180 and Nightingale NMR platforms.

Installation

git clone https://github.com/tomszar/adni_metabolomics.git

cd adni_metabolomics
pip install .

In the folder with the required datasets, simply run:

clean_files

And 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