In tumor tissue, underlying genomic instability can lead to DNA copy number alterations, e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the genome, whereas recurrent alterations are observed in the same genomic region across multiple independent samples, perhaps because they provide a selective growth advantage. This package implements the DiNAMIC procedure for assessing the statistical significance of recurrent DNA copy number aberrations (Bioinformatics (2011) 27(5) 678 - 685).
DNA copy number changes (gains and losses) are commonly seen in tumor tissue. Some copy number changes provide a selective growth advantage, and these are observed in the same genomic region across multiple samples. These copy number changes are termed recurrent. In contrast, sporadic copy number changes that occur randomly throughout the genome because of underlying genomic instability are less likely to have biological relevance. The dinamic R package was designed to assess the statistical significance of recurrent DNA copy number aberrations using the cyclic shift permutation scheme.
Please refer to the vignette.