PPTC PDX Classifier and Correlation Figures

Author:	Jo Lynne Rokita, Gregory P. Way
Contact:	Jo Lynne Rokita ([email protected])
Organization:	CHOP
Status:	complete
Date:	2024-12-20

Introduction

Here, we provide scripts to enable reproducible generation of Manuscript Figures 4 and S4. This repo contains code for:

1. Creating ROC Curves from classifier data
2. Creating gene and variant level classification data
3. Creating correlation matrices for classification scores, tumor mutation burden, and mutational signatures.

Details

• RUN-classifier-analyses.R
• classifier-plots-revision.R
• corplots.R
• cormat.R
• install.packages.R
• mutation-color-function.R
• theme.R

Software Requirements

R 3.4.3

Pipeline

# How to run:
# Download github repository in your home directory (~/)
git clone https://github.com/marislab/pptc-pdx-classifier-analysis.git

# Run script to create pie chart
Rscript ~/pptc-pdx-classifier-analysis/R/RUN-classifier-analyses.R

Results

Results will appear in the results folder