Reproducible data, example subsets, and analysis pipeline for the extended TAaCGH study of breast cancer genomic and transcriptomic profiles

This repository contains the R-based computational framework used to implement and extend the TAaCGH (Tumor Array CGH) pipeline for the associated study. The materials provide a clear and reproducible workflow, taking the user from data preprocessing through survival analysis and subtype-specific modeling. When applied to the referenced publicly available datasets, the scripts reproduce all analyses reported in the manuscript, including maximally selected rank statistic (MaxStat) calculations and region-to-gene mapping steps. The workflow is designed to run end-to-end and produces a consistent set of outputs, such as multiple-testing-adjusted significance tables, genomic interval annotations, and gene biotype summaries. In addition, the pipeline generates diagnostic plots and gene metadata that support interpretation of subtype-specific genomic patterns. Detailed instructions describing the directory structure and execution steps are provided in the accompanying README to support reprod..., , **TAaCGH-Extension-main.zip** contains all files required to reproduce the analyses and results presented in the associated study. This archive includes the complete codebase and documentation needed to execute the extended TAaCGH pipeline. Users can run the scripts directly to regenerate the results and figures described in the manuscript. A public, version-controlled copy of this repository is also available on GitHub at: [https://github.com/Arsuaga-Vazquez-Lab/TAaCGH-Extension](https://github.com/Arsuaga-Vazquez-Lab/TAaCGH-Extension). Detailed explanations of each file, folder structure, and workflow components are provided in the included README.

## Repository Overview

Horlings et al. dataset. Original data from Horlings et al. (2010) are available in the supplementary material of the publication at [https://doi.org/10.1158/1078-0432.CCR-09-0709](https://doi.org/10.1158/1078-0432.CCR-09-0709). A script to preprocess the dataset from the supplementary material is provided in the co...,