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.