BOBaFIT

BOBaFIT refits and corrects the diploid region in copy number profiles using a clustering algorithm to identify pathology-specific normal (diploid) chromosomes and then uses their copy number signal to refit the whole profile.

Key Features:

• DRrefit: Main function that performs the refitting of copy number profiles based on identified diploid chromosomes.
• ComputeNormalChromosome: Identifies pathology-specific normal chromosomes through clustering analysis.
• PlotCluster: Generates visualizations of clustering results for quality assessment and interpretation.

Scientific Applications:

• Copy number profile correction: Corrects inaccurate diploid region assignments in tumor copy number profiles where the baseline ploidy has been misidentified.
• Cancer genomics analysis: Enables accurate identification of copy number alterations by establishing correct diploid baselines in pathology samples with complex karyotypes.

Methodology:

BOBaFIT applies a clustering algorithm to identify pathology-specific normal (diploid) chromosomes from copy number profiles, then uses the copy number signal from these identified normal chromosomes to refit the entire profile.