Rseg

Rseg detects copy number alterations (CNAs) in tumor samples with adaptive thresholding and normalization artifact correction.

Key Features:

• Sample-Specific Gain/Loss Thresholds: Allows user-defined thresholds for CNA calling to accommodate intra-tumor heterogeneity and normal cell contamination.
• RMA Normalization Artifact Correction: Adjusts copy-number ratios to correct artifacts introduced by Robust Multichip Average (RMA) normalization in non-changed genomic elements.

Scientific Applications:

• Cancer Copy Number Analysis: Identifies true genomic gains and losses while minimizing technical artifacts in tumor CNA studies.

Methodology:

Rseg applies interactive, sample-specific thresholding for gain and loss detection and incorporates correction procedures for RMA-induced normalization biases to improve accuracy of copy number alteration analysis.