This repo contains a series of analyses that are included in Clonal hematopoiesis is driven by aberrant activation of TCL1A. For questions, contact Josh Weinstock. The analyses were largely performed in Rmarkdown files. Please see the Rmarkdown documentation for executing these files.
For running PACER on your own data, you will first need passenger count variant calls. Code for our passenger count pipeline is available here. Note that this pipeline assumes thats you have whole genome Mutect2 calls.
Please see here for our analyses on estimating driver gene fitness estimates.
See here for our analysis of our clonal expansion estimates in WHI carriers with multiple mutational assessments.
See here for our application of aBayesian logistic growth model to the WHI cohort.
See here for PACER-HB development and analyses.
See here for our analysis that performs finemapping of the TCL1A locus using SuSIE.
See here for a repo containing code to run simulations of passenger count accumulation in HSCs.
Please see the data availability statement in the paper. The data required to reproduce these analysis is available through dbGaP.
An renv lock file is provided, which states the R version and packages required.
This analysis has only been tested on Ubuntu 18.04.
This code is dual-licensed. See the license for further details.