INSPIRE cfMeDIP-seq Paper Reproducible Report

In the interest of transparency, openness, and reproducibility, this report contains the analysis code which generates all of the figures and numerical results for the manuscript entitled Early changes in tumor-agnostic cell-free methylomes and fragmentomes predict outcomes in patients with solid tumors treated with pembrolizumab. In it, we report on the results of cell-free methylated DNA immunoprecipitation and sequencing (cfMeDIP-seq) from the investigator-initiated phase 2 study of pembrolizumab immunological response evaluation (INSPIRE).

Instructions

Using Rstudio or the knitr package in R, all results reported in the manuscript can be regenerated in full using the RMarkdown file, INSPIRE-cfMeDIP-Paper-Code.Rmd.

All of the processed, deidentified data are stored in figure_data.Rds as dataframes and are attached to the environment in the setup block. Our nomenclature is variable names starting with df to denote source data tables and plotdata for processed dataframes used as intermediates to generate figures. Variables that start with val denote numeric values, many of which are reported in the final results.

To view the results of the analysis, download INSPIRE-cfMeDIP-Paper-Code.html.

To run the analysis yourself, follow these steps:

1. Install R - https://www.r-project.org/
2. Install Rstudio - https://posit.co/products/open-source/rstudio/
3. Clone this repository in the terminal with git clone https://github.com/pughlab/paper-inspire-cfmedip.git OR download this repository as a ZIP file.
4. Open INSPIRE-cfMeDIP-Paper-Code.Rmd in Rstudio.
5. Install knitr, rmdformats and all of the dependency packages which are called by library() function in the setup block.
6. Run all blocks or knit the R Markdown document.