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PPTC PDX Oncoprint Generation

Authors: Jo Lynne Rokita
Alvin Farrel
Khushbu Patel
Contact: Jo Lynne Rokita (rokita@email.chop.edu)
Organization: CHOP
Status: Complete
Date: 2024-10-24

Introduction

Here, we provide scripts to enable reproducible generation of Manuscript Figure 2: oncoprints by PDX histology and Figure 3: co-oncoplots for diagnosis/relapse samples in neuroblastoma, BCP-ALL, T-ALL, and osteosarcoma. This repo contains code for:

  1. Create expanded oncoprint matrices used to reproduces Figure 2 and 3

Details

  • RUN-create-full-oncoprint-revision.R
  • load-maf-maftools.R
  • cluster-scores.R
  • merge-mut-CN-fusion-matrices.R
  • co-oncoplots.R
  • merge-mut-CN-matrices.R
  • create-CN-matrices.R
  • mutation-color-function.R
  • create-complexheat-oncoprint-revision.R
  • reformat-CN-matrix-to-df.R
  • create-mut-matrices.R
  • reformat-clinical.R
  • create-mut-sigs-matrix.R
  • reformat-fusion-as-matrix.R
  • demog-color-function.R
  • reformat-fusion-for-maf-revision.R
  • install-packages.R

Software Requirements

R 3.4.3

Pipeline

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

# Run script to create pie chart
Rscript ~/create-pptc-pdx-oncoprints/R/RUN-create-full-oncoprint-revision.R

Results

Results will appear in the onco-out folder