Plasma Metabolomic Profiling in Patients with Rheumatoid Arthritis Identifies Biochemical Features Predictive of Quantitative Disease Activity

Arthritis Research & Therapy (2021): https://arthritis-research.biomedcentral.com/articles/10.1186/s13075-021-02537-4

Authors: Benjamin Hur, Vinod K. Gupta, Harvey Huang, Kerry A. Wright, Kenneth J. Warrington, Veena Taneja, John M. Davis III, and Jaeyun Sung

Contact: hur.benjamin@mayo.edu Corresponding Author: sung.jaeyun@mayo.edu

1. Differentially Abundant metabolites

src/linear_model_r1/MLR_R_categorical_diff_2class_v2.r

analysis/differential_abundance_public/2class/run.sh

2. Feature selection for quantitative disease activity of RA

src/machine_learning_public/All_IN_ONE_FeatureSelection_CV_LOO.py

analysis/selection_scheme_public/run.sh

3. Other statistics

Investigation of drugs (csDMARD, TNFi-bDMARD, non-TNFi-bDMARD, MTX, PRED) that affected the abundance of metabolites.

src/statistics/drug_effect_lmer_R.ipynb

Differentially abundant metabolites related test. Investigates whether confounding effects (drug, smoke, age, etc) differs between higher and lower disease activity.

src/statistics/ftest_comfounds.ipynb

Investigation of prescription (csDMARD, TNFi-bDMARD, non-TNFi-bDMARD, MTX, PRED) differences between visit 1 and visit 2.

code/statistics/mcnemar_test_R.ipynb

DATA

preprocessed data: Training datset (n=128)

data/discovery_cohort

preprocessed data: Test dataset (n=12)

data/validation_cohort