Inference of Chromosome Selection Parameters and Missegregation Rate in Cancer from DNA-Sequencing Data

Installation

The CINner simulator [1] can be installed with

devtools::install_github("dinhngockhanh/CINner")

To perform CINner-based inference of chromosome selection parameters and missegregation rate in [2], the functions in the R folder must be loaded, then functions in the vignettes folder (detailed below) can be performed.

Result vignettes

Our inference method uses CINner to infer chromosome selection parameters and missegregation rate:

The file vignettes/Inference for selection and missegregation parameters.r reproduces results from our inference method for selection parameters and missegregation rate from a mixture of bulk and single-cell DNA sequencing data (Results sections 2 & 3, [2]):

The files vignettes/Sensitivity of bulk DNA sample count.r and vignettes/Sensitivity of single-cell DNA sample count.r reproduce our sensitivity studies to analyze the performance of the inference method with respect to the number of bulk and single-cell samples, respectively (Results section 4, [2]).

The file vignettes/Study of MEDICC2 inference.r studies the accuracy of single-cell statistics based on copy number profiles and phylogenies inferred by MEDICC2, compared to CINner ground-truth (Results section 5, [2]).

References

1. Dinh KN, Vázquez-García I, Chan A, Malhotra R, Weiner A, McPherson AW, Tavaré S. CINner: modeling and simulation of chromosomal instability in cancer at single-cell resolution. bioRxiv. 2024.
2. Xiang Z, Liu Z, Dinh KN. Inference of chromosome selection parameters and missegregation rate in cancer from DNA-sequencing data. bioRxiv. 2024.