README.md

In argymeg/breakclone: Estimating clonal relatedness probability between tumour pairs

[!NOTE] This repository contains the original breakclone package described in:

Lips, E.H., Kumar, T., Megalios, A. et al. Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer. Nat Genet 54, 850–860 (2022). https://doi.org/10.1038/s41588-022-01082-3

It is no longer updated or maintained. Ongoing development is hosted at: https://github.com/Sawyer-s-Group/breakclone.

breakclone

Breakclone is a package for assessing clonal relationships of tumour pairs based on copy number or mutation data.

Example

This is a basic example of usage with copy number data:

library(breakclone)
table <- readAlleleSpecific("/path/to/data")
pairs <- data.table::fread("/path/to/sample/sheet")
reference <- makeReferenceCN(table, pairs)
results <- calculateRelatednessCn(table, pairs, reference)
plotScoresDensity(reference, results)

This is a very similar example with mutation data:

library(breakclone)
table <- readVCFMutations("/path/to/data")
pairs <- data.table::fread("/path/to/sample/sheet")
reference <- makeReferenceMutations(table, pairs)
results <- calculateRelatednessMutations(table, pairs, reference)
plotScoresDensity(reference, results)

argymeg/breakclone documentation built on Nov. 9, 2024, 7:12 p.m.