Interplay between chromosomal alterations and gene mutations in clonal hematopoiesis

Code and Data for Gao et al. Nature Communications 2021.

Directory structure

└─ notebooks/:
|   └─ ch_cnv_figures.html: Analysis code and scripts to reproduce figures
|   └─ plot_forest.R: helper script to create forest plots
|   └─ table_one.R: helper script to tally demographics
└─ data/:
|   └─ clinical_data.tsv: Patient blood count, demographics, and treatment data
└─ facets-ch/:
|   └─ R/: Source code for the FACETS-CH algorithm
|   └─ tests/:
|   |   └─ data/: example input data and commandline script for FACETS-CH

Analysis notebooks

An interactive jupyter notebook is provided to reproduce the analyses in the paper. First install Jupyter and then launch the notebook ch_cnv_figures.ipynb.

Correction (03/22/2021)

The confidence level of confidence intervals (as specified in the figure legends) in Figure 1f, Figure 2b-c, Supplementary Figure 9b, and Supplementary Figure 13 are 90% instead of 95%. No conclusions in the main or supplementary text are affected. Code are added in the notebook for constructing 95% confidence intervals in the above figures.

FACETS-CH algorithm

Code to implement the FACETS-CH algorithm is provided here under the facets-ch subfolder.