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TreeSummarizedExperiment: a S4 class for data with hierarchical structure [version 2; peer review: 2 approved, 1 approved with reservations]

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العنوان: TreeSummarizedExperiment: a S4 class for data with hierarchical structure [version 2; peer review: 2 approved, 1 approved with reservations]
المؤلفون: Ruizhu Huang, Charlotte Soneson, Felix G.M. Ernst, Kevin C. Rue-Albrecht, Guangchuang Yu, Stephanie C. Hicks, Mark D. Robinson
المصدر: F1000Research, Vol 9 (2021)
بيانات النشر: F1000 Research Ltd, 2021.
سنة النشر: 2021
المجموعة: LCC:Medicine
LCC:Science
مصطلحات موضوعية: Medicine, Science
الوصف: Data organized into hierarchical structures (e.g., phylogenies or cell types) arises in several biological fields. It is therefore of interest to have data containers that store the hierarchical structure together with the biological profile data, and provide functions to easily access or manipulate data at different resolutions. Here, we present TreeSummarizedExperiment, a R/S4 class that extends the commonly used SingleCellExperiment class by incorporating tree representations of rows and/or columns (represented by objects of the phylo class). It follows the convention of the SummarizedExperiment class, while providing links between the assays and the nodes of a tree to allow data manipulation at arbitrary levels of the tree. The package is designed to be extensible, allowing new functions on the tree (phylo) to be contributed. As the work is based on the SingleCellExperiment class and the phylo class, both of which are popular classes used in many R packages, it is expected to be able to interact seamlessly with many other tools.
نوع الوثيقة: article
وصف الملف: electronic resource
اللغة: English
تدمد: 2046-1402
Relation: https://f1000research.com/articles/9-1246/v2; https://doaj.org/toc/2046-1402
DOI: 10.12688/f1000research.26669.2
URL الوصول: https://doaj.org/article/2145c95bf9414a21ba337d5460a6928c
رقم الأكسشن: edsdoj.2145c95bf9414a21ba337d5460a6928c
قاعدة البيانات: Directory of Open Access Journals
الوصف
تدمد:20461402
DOI:10.12688/f1000research.26669.2