التفاصيل البيبلوغرافية
| العنوان: |
Overview of SubMARine in extended mode. |
| المؤلفون: |
Linda K. Sundermann (10005012), Jeff Wintersinger (8442321), Gunnar Rätsch (54319), Jens Stoye (26927), Quaid Morris (51067) |
| سنة النشر: |
2021 |
| المجموعة: |
Smithsonian Institution: Digital Repository |
| مصطلحات موضوعية: |
Cell Biology, Genetics, Molecular Biology, Pharmacology, Biotechnology, Evolutionary Biology, Ecology, Developmental Biology, Cancer, Infectious Diseases, Plant Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, clone trees, clone tree validity conditions, partially-defined clone tree, lung cancer dataset, MAR, Subclonal reconstruction methods cl., subclonal copy number aberrations, freely-available open-source code, Maximally-Constrained Ancestral Rec., clone tree reconstruction methods, prostate cancer dataset, clone tree |
| الوصف: |
The extended version of SubMARine takes the subclonal frequency matrix ϕ , CNAs as copy number changes in the matrices Δ C A and Δ C B , assigned to subclones, segments and parental alleles in the vectors λ c , σ c and π c , SSMs assigned to segments and subclones in the vectors σ s and λ s , and the impact matrix as input to build the ancestry matrix Z and the SSM phasing vector π s . At first, the monotonicity restriction is checked to hold on the CNAs. Then, in the preprocessing phase, the germline rule is introduced and trivial relationships ( Z ( k , k ′) = 0 for k ′ ≤ k ) are set. Afterwards, SubMARine starts the main phase, ensuring that the partial tree rule is applied each time a relationship is updated. First, the equivalence rule based on Eq (13) in Section IV.3 in S1 Text is propagated, leading to 1’s in Z , together with those equivalence and lost allele rules that update SSM phasing. Second those equivalence and lost allele rules that lead to 0’s in Z and the crossing rule are used. Third, the general sum rule is propagated with Subpoplar, which also applies the equivalence, lost allele and partial tree rules whenever necessary. The method converges, when no more subclonal relationships and SSM phases can be updated. The output consists of the ancestry matrix Z , the SSM phasing vector π s and the possible parent matrix τ , created by Subpoplar. The user can also define additional constraints on Z and on π s . Both types of constraints are applied after the preprocessing step and before the main phase starts. When user-constraints on Z are set, the partial tree rule is already propagated before the main phase. Whenever a constraint cannot be satisfied, SubMARine terminates and indicates what led to the conflict. (PDF) |
| نوع الوثيقة: |
article in journal/newspaper |
| اللغة: |
unknown |
| Relation: |
https://figshare.com/articles/journal_contribution/Overview_of_SubMARine_in_extended_mode_/13609626 |
| DOI: |
10.1371/journal.pcbi.1008400.s005 |
| الاتاحة: |
https://doi.org/10.1371/journal.pcbi.1008400.s005 |
| Rights: |
CC BY 4.0 |
| رقم الانضمام: |
edsbas.E9718F49 |
| قاعدة البيانات: |
BASE |