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>. A manuscript based on DiNAMIC.Duo is currently under development.
||R (≥ 3.5.0)
||biomaRt, dinamic, plyr, reticulate
||Vonn Walter [aut,
Hyo Young Choi
Yan Gao [aut],
David Neil Hayes
||Vonn Walter <vwalter1 at pennstatehealth.psu.edu>
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