Package: DiNAMIC.Duo 1.0.2

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>.

Authors:Vonn Walter [aut, cre], Hyo Young Choi [aut], Xiaobei Zhao [aut], Yan Gao [aut], David Neil Hayes [aut]

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Exports:cyclicNullRcyclicShiftColRdataPrepgenomeChrPlotgenomePlotpeelingOnepeelingOneIteratepeelingTwopeelingTwoIterateresultsProcess

Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdigestdinamicdplyrfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDatagluehmshttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsRcpprlangRSQLiteS4VectorsstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrxml2XVectorzlibbioc