Code for Predicting MIEs from Gene Expression and Chemical Target Labels with Machine Learning (MIEML)

Installation

System Requirements

This package provides scripts in R. For training models in the R package Caret, only R is required.

R Install

All code in this package has been tested on R 3.6.0, but any version of R 3.x should be sufficient. Package versions may have an impact due to changes in functionality or API.
The following R libraries are also required to use all features of the R code:

• caret - Required for training binary classifiers. Code has been tested with v6.0-83
• data.table - Required for internal data handling. Code has been tested with v1.12.2
• dplyr - Required for internal data handling. Code has been tested with v0.8.3.
• rlist - Required for internal data handling. Code has been tested with v0.4.6.1.
• cmapR - Required for importing LINCS L1000 gene expression data internally. Code has been tested with vcmapR_1.0.1.
• parallel - Required for parallelizing model training. Code has been tested with v3.6.0.
• doParallel - Required for parallelizing model training. Code has been tested with v1.0.15.
• foreach - Required for parallelizing model training. Code has been tested with v1.4.7.

Additional Datasets

Classifier training relies on several publicly available data sets:

• LINCS L1000 Phase 1 release - GEO entry for LINCS phase 1
• LINCS L1000 Phase 2 release - GEO entry for LINCS phase 2
• RefChemDB Supplemental Information - RefChemDB table - supplemental table 12 should be exported and converted to .csv
• MSigDB gene sets - MSigDB gene sets required if training classifiers using GSEA and pathway scoring - this file should be converted to .txt.

Installing the MIEML package

Currently, it is recommended to clone the entire repo to a user or analysis directory by running:

git clone https://github.com/USEPA/CompTox-MIEML.git (/path/to/analysis)

Installing the HTTr_pathway package

This is only recommended if users wish to train classifiers using pathway scores. Currently, it is recommended to clone the entire repo to a user or analysis directory by running:

git clone https://github.com/USEPA/CompTox-httrpathway.git (/path/to/analysis)

Running an Analysis

Vignette is located at mieml/notebooks/ML_functions_vignette.Rmd Modules are in: mieml/scripts/

Version History

(12/20/21)

• Created new (current) branch for public release of MIEML version used to generate code in initial project-associated publication.

(2/17/22)

• Revised vignette and primary MIEML functions for ease of use

(3/2/22)

• Revised README and vignette for public repo

Contributors

• Logan J. Everett
• Joseph L. Bundy