/Gao_NC_CH

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

Primary LanguageJupyter Notebook

Interplay between chromosomal alterations and gene mutations in clonal hematopoiesis

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

DOI

image

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.