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 reproducibility and reuse.