This repository contains the code for the analyses and figures for our preprint "Defining the extent of gene function using ROC curvature".

Requirements

The code contains a mixture of shell scripts (downloading data), Python (analysis of ROC curve) and R (data handling, analysis of results and figure generation). The code was tested and run on a Linux server with CentOS7, Python 3.7.3 and R 4.0.5.

To run scripts on a command line, use sh <shell_script>.sh, python <python_script>.py, Rscript <shell_script>.R.

Required packages for Python are: numpy, pandas, seaborn, matplotlib.pyplot, scipy.stats, scipy.io, scipy.sparse, sklean.metrics, h5py.

Required packages for R are: tidyverse, Matrix, org.Mm.eg.db, rhdf5, rjson, ontologyIndex, ggupset, MetaMarkers (https://github.com/gillislab/MetaMarkers), SingleCellExperiment, ROCR.

Description of files and directories

Here is an overall description of the elements found in the root directory:

• 01_data: this directory contains all the scripts needed to download and pre-process the data for subsequent analyses (see 01_data/README for further details).
• 02_markers: this directory contains all the scripts needed to reproduce all analyses related to marker gene FECs in single-cell data (see 02_markers/README for further details).
• 03_coexp_ppi: this directory contains all the scripts needed to reproduce all analyses related to FECs extracted from functional predictions based on PPI and co-expression networks (see 03_coexp_ppi/README for further details).
• 04_literature: this directory contains all the scripts needed to reproduce all analyses related to FECs extracted from published ROC curves (see 04_literature/README for further details).
• 05_simulation: this directory contains all the scripts needed to reproduce all analyses related to FECs as seen in simulation models (gaussian mixture model, network model).
• pyroc: this directory contains the Python module used to analyze ROC curves (e.g., extraction of FECs). The module is used by other scripts in the project, there is nothing to run in this directory.
• data.py: utility script that makes data available to Python scripts.
• data.R: utility script that makes data available to R scripts.