CINmetrics

CINmetrics computes six chromosomal instability (CIN) scores in R to quantify and compare structural and numerical chromosomal alterations associated with cancer and other diseases.

Key Features:

• Comprehensive scoring system: Calculates six distinct chromosomal instability scores to capture multiple aspects of CIN.
• Comparative analysis: Enables direct comparison between different CIN scores to assess concordance and differences among metrics.
• Integration of established metrics: Implements multiple established chromosomal instability metrics within a single R package and standardizes their calculation.
• Clinical data application: Demonstrated on breast cancer data from The Cancer Genome Atlas (TCGA) to explore CIN in real-world datasets.
• Phenotype association support: Facilitates analysis of associations between CIN scores and clinical or biological phenotypes.

Scientific Applications:

• Disease characterization: Study diseases characterized by genomic instability, including cancer and neurodegenerative disorders.
• Cancer research (TCGA breast cancer): Assess relationships between CIN scores and clinical or biological phenotypes in TCGA breast cancer data.
• Metric evaluation across studies: Compare CIN metrics across datasets or studies to standardize CIN assessment and enable cross-study analyses.

Methodology:

Implements and integrates multiple established chromosomal instability metrics within an R package to compute six CIN scores and enable their comparison across datasets.