DiNAMIC.Duo - Finding Recurrent DNA Copy Number Alterations and Differences
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. Here we use cyclic shift permutations to identify
recurrent copy number alterations in a single cohort or
recurrent copy number differences in two cohorts based on a
common set of genomic markers. Additional functionality is
provided to perform downstream analyses, including the creation
of summary files and graphics. DiNAMIC.Duo builds upon the
original DiNAMIC package of Walter et al. (2011)
<doi:10.1093/bioinformatics/btq717> and leverages the theory
developed in Walter et al. (2015) <doi:10.1093/biomet/asv046>.
An article describing DiNAMIC.Duo by Walter et al. (2022) can
be found at <doi: 10.1093/bioinformatics/btac542>.
