TreeSummarizedExperiment: a S4 class for data with hierarchical structure [version 2; peer review: 3 approved]

Ruizhu Huang, Charlotte Soneson, Felix G.M. Ernst, Kevin C. Rue-Albrecht, Guangchuang Yu, Stephanie C. Hicks, Mark D. Robinson

Research output: Contribution to journalArticlepeer-review

Abstract

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

Original languageEnglish (US)
Pages (from-to)2-43
Number of pages42
JournalF1000Research
Volume9
DOIs
StatePublished - 2021

Keywords

  • SummarizedExperiment
  • hierarchical structure
  • microbiome
  • tree

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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