R Code for Analyses. This is a zip file containing all of the R code used to perform simulations and to analyze the breast cancer data. (ZIP 407 kb)

Machine Learning pipeline used to provide toxicity prediction in FunTox-Networks

01_DATA # preprocessing and filtering of raw activity data from ChEMBL
- Chembl_v25 # latest activity assay data set from ChEMBL (retrieved Nov 2019)
- filt_stats.R # Filtering and preparation of raw data
- Filtered # output data sets from filt_stats.R
- toxicity_direction.csv # table of toxicity measurements and their proportionality to toxicity

02_MolDesc # Calculation of molecular descriptors for all compounds within the filtered ChEMBL data set
- datastore # files with all compounds and their calculated molecular descriptors based on SMILES
- scripts
- calc_molDesc.py # calculates for all compounds based on their smiles the molecular descriptors
- chemopy-1.1 # used python package for descriptor calculation as decsribed in: https://doi.org/10.1093/bioinformatics/btt105

03_Averages # Calculation of moving averages for levels and organisms as required for calculation of Z-scores
- datastore # output files with statistics calculated by make_Z.R
- scripts
-make_Z.R # script to calculate statistics to calculate Z-scores as used by the regression models

04_ZScores # Calculation of Z-scores and preparation of table to fit regression models
- datastore # Z-normalized activity data and molecular descriptors in the form as used for fitting regression models
- scripts
-calc_Ztable.py # based on activity data, molecular descriptors and Z-statistics, the learning data is calculated

05_Regression # Performing regression. Preparation of data by removing of outliers based on a linear regression model. Learning of random forest regression models. Validation of learning process by cross validation and tuning of hyperparameters.

- datastore # storage of all random forest regression models and average level of Z output value per level and organism (zexp_*.tsv)
- scripts
- data_preperation.R # set up of regression data set, removal of outliers and optional removal of fields and descriptors
- Rforest_CV.R # analysis of machine learning by cross validation, importance of regression variables and tuning of hyperparameters (number of trees, split of variables)
- Rforest.R # based on analysis of Rforest_CV.R learning of final models

rregrs_output
# early analysis of regression model performance with the package RRegrs as described in: https://doi.org/10.1186/s13321-015-0094-2

Causal effect estimates using Radial MVMR with and without outlier removal with varying levels of balanced pleiotropy.

MLR models of age at onset of T1D after removing outliers (N = 354).